From b6ad55f4d2c702ecc904d6b40b4b35b2463c895a Mon Sep 17 00:00:00 2001
From: nikostr <nikostr@users.noreply.github.com>
Date: Thu, 23 May 2024 11:45:35 +0200
Subject: [PATCH 01/41] fix: bamcoverage without effective genome size (#2941)

Running deeptools bamcoverage without an effective genome size did not
work previously. This PR fixes that issue.

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] I confirm that:

For all wrappers added by this PR,

* there is a test case which covers any introduced changes,
* `input:` and `output:` file paths in the resulting rule can be changed
arbitrarily,
* either the wrapper can only use a single core, or the example rule
contains a `threads: x` statement with `x` being a reasonable default,
* rule names in the test case are in
[snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell
what the rule is about or match the tools purpose or name (e.g.,
`map_reads` for a step that maps reads),
* all `environment.yaml` specifications follow [the respective best
practices](https://stackoverflow.com/a/64594513/2352071),
* the `environment.yaml` pinning has been updated by running
`snakedeploy pin-conda-envs environment.yaml` on a linux machine,
* wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`),
* all fields of the example rules in the `Snakefile`s and their entries
are explained via comments (`input:`/`output:`/`params:` etc.),
* `stderr` and/or `stdout` are logged correctly (`log:`), depending on
the wrapped tool,
* temporary files are either written to a unique hidden folder in the
working directory, or (better) stored where the Python function
`tempfile.gettempdir()` points to (see
[here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir);
this also means that using any Python `tempfile` default behavior
works),
* the `meta.yaml` contains a link to the documentation of the respective
tool or command,
* `Snakefile`s pass the linting (`snakemake --lint`),
* `Snakefile`s are formatted with
[snakefmt](https://github.com/snakemake/snakefmt),
* Python wrapper scripts are formatted with
[black](https://black.readthedocs.io).
* Conda environments use a minimal amount of channels, in recommended
ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as
conda-forge should have highest priority and defaults channels are
usually not needed because most packages are in conda-forge nowadays).
---
 bio/deeptools/bamcoverage/test/Snakefile | 12 ++++++++++++
 bio/deeptools/bamcoverage/wrapper.py     |  2 +-
 test.py                                  | 15 +++++++++++++++
 3 files changed, 28 insertions(+), 1 deletion(-)

diff --git a/bio/deeptools/bamcoverage/test/Snakefile b/bio/deeptools/bamcoverage/test/Snakefile
index 26907be6a5e..f517a890cc6 100644
--- a/bio/deeptools/bamcoverage/test/Snakefile
+++ b/bio/deeptools/bamcoverage/test/Snakefile
@@ -28,3 +28,15 @@ rule test_deeptools_bamcoverage_default_eff_len:
         "logs/coverage_efault_eff_len.log",
     wrapper:
         "master/bio/deeptools/bamcoverage"
+
+
+rule test_deeptools_bamcoverage_no_params:
+    input:
+        bam="a.sorted.bam",
+        bai="a.sorted.bam.bai",
+    output:
+        "a.coverage_no_params.bw",
+    log:
+        "logs/coverage.log",
+    wrapper:
+        "master/bio/deeptools/bamcoverage"
diff --git a/bio/deeptools/bamcoverage/wrapper.py b/bio/deeptools/bamcoverage/wrapper.py
index d3b4925efbf..e5d607e2cd8 100644
--- a/bio/deeptools/bamcoverage/wrapper.py
+++ b/bio/deeptools/bamcoverage/wrapper.py
@@ -100,7 +100,7 @@
     },
 }
 
-effective_genome_size = snakemake.params.get("effective_genome_size")
+effective_genome_size = snakemake.params.get("effective_genome_size", "")
 if not effective_genome_size:
     genome = snakemake.params.get("genome")
     read_length = snakemake.params.get("read_length")
diff --git a/test.py b/test.py
index dd60f302944..cab6ba917b9 100644
--- a/test.py
+++ b/test.py
@@ -2870,6 +2870,21 @@ def test_deeptools_bamcoverage_eff():
     )
 
 
+@skip_if_not_modified
+def test_deeptools_bamcoverage_no_params():
+    run(
+        "bio/deeptools/bamcoverage",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "a.coverage_no_params.bw",
+            "--use-conda",
+            "-F",
+        ],
+    )
+
+
 @skip_if_not_modified
 def test_deeptools_alignmentsieve():
     run(

From 5b3ca20635bd0e427a548e68cd8a40fdb0047f10 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 24 May 2024 01:26:27 +0000
Subject: [PATCH 02/41] perf: autobump bio/bowtie2/build (#2942)

Automatic bump of bio/bowtie2/build.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 .../build/environment.linux-64.pin.txt        | 39 +++++++++----------
 bio/bowtie2/build/environment.yaml            |  2 +-
 2 files changed, 20 insertions(+), 21 deletions(-)

diff --git a/bio/bowtie2/build/environment.linux-64.pin.txt b/bio/bowtie2/build/environment.linux-64.pin.txt
index 024ff3708a4..70e1fd1b6fb 100644
--- a/bio/bowtie2/build/environment.linux-64.pin.txt
+++ b/bio/bowtie2/build/environment.linux-64.pin.txt
@@ -3,36 +3,35 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.11.17-hbcca054_0.conda#01ffc8d36f9eba0ce0b3c1955fa780ee
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_3.conda#937eaed008f6bf2191c5fe76f87755e9
-https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce
-https://conda.anaconda.org/conda-forge/noarch/tzdata-2023d-h0c530f3_0.conda#8dee24b8be2d9ff81e7bd4d7d97ff1b0
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_3.conda#7124cbb46b13d395bdde68f2d215c989
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda#10569984e7db886e4f1abc2b47ad79a1
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_3.conda#23fdf1fef05baeb7eadc2aed5fb0011f
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
 https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda#cc47e1facc155f91abd89b11e48e72ff
+https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d
 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
 https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-hd590300_2.conda#d66573916ffcf376178462f1b61c941e
 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7
 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_2.conda#7dbaa197d7ba6032caf7ae7f32c1efa0
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.0-hd590300_1.conda#603827b39ea2b835268adb8c821b8570
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
-https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.44.2-h2797004_0.conda#3b6a9f225c3dbe0d24f4fedd4625c5bf
-https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.4-h232c23b_1.conda#53e951fab78d7e3bab40745f7b3d1620
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.3-h2797004_0.conda#b3316cbe90249da4f8e84cd66e1cc55b
+https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.7-hc051c1a_0.conda#5d801a4906adc712d480afc362623b59
 https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda#f2cfec9406850991f4e3d960cc9e3321
 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
-https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
-https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
-https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.9.3-default_h554bfaf_1009.conda#f36ddc11ca46958197a45effdd286e45
-https://conda.anaconda.org/conda-forge/linux-64/python-3.10.13-hd12c33a_1_cpython.conda#ed38140af93f81319ebc472fbcf16cca
-https://conda.anaconda.org/conda-forge/noarch/setuptools-69.0.3-pyhd8ed1ab_0.conda#40695fdfd15a92121ed2922900d0308b
-https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.11.0-h00ab1b0_0.conda#fde515afbbe6e36eb4564965c20b1058
-https://conda.anaconda.org/conda-forge/noarch/wheel-0.42.0-pyhd8ed1ab_0.conda#1cdea58981c5cbc17b51973bcaddcea7
-https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.3-py310ha0a81b8_0.tar.bz2#b3f4f67b4edd879fd02b496833edc9be
-https://conda.anaconda.org/conda-forge/noarch/pip-23.3.2-pyhd8ed1ab_0.conda#8591c748f98dcc02253003533bc2e4b1
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
+https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h5622ce7_1001.conda#fc2d5b79c2d3f8568fbab31db7ae02f3
+https://conda.anaconda.org/conda-forge/linux-64/python-3.12.3-hab00c5b_0_cpython.conda#2540b74d304f71d3e89c81209db4db84
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda#c8ddb4f34a208df4dd42509a0f6a1c89
+https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h297d8ca_1.conda#3ff978d8994f591818a506640c6a7071
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae
+https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.4-he20e202_0.tar.bz2#c9e131332789019b1b70018011f82035
+https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67
diff --git a/bio/bowtie2/build/environment.yaml b/bio/bowtie2/build/environment.yaml
index f4f4ca331ab..642bb4a2079 100644
--- a/bio/bowtie2/build/environment.yaml
+++ b/bio/bowtie2/build/environment.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bowtie2 =2.5.3
+  - bowtie2 =2.5.4

From 9228479896c2410ae6a58849bf59e5f01bc5e712 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 24 May 2024 01:29:13 +0000
Subject: [PATCH 03/41] perf: autobump bio/bismark/bam2nuc (#2943)

Automatic bump of bio/bismark/bam2nuc.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 .../bam2nuc/environment.linux-64.pin.txt      | 38 ++++++++++---------
 bio/bismark/bam2nuc/environment.yaml          |  2 +-
 2 files changed, 21 insertions(+), 19 deletions(-)

diff --git a/bio/bismark/bam2nuc/environment.linux-64.pin.txt b/bio/bismark/bam2nuc/environment.linux-64.pin.txt
index 904bacb38de..24fb8348f53 100644
--- a/bio/bismark/bam2nuc/environment.linux-64.pin.txt
+++ b/bio/bismark/bam2nuc/environment.linux-64.pin.txt
@@ -3,14 +3,16 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_14.conda#38d211c448a67f12fe693fe25df4da23
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
-https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce
-https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda#10569984e7db886e4f1abc2b47ad79a1
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-4_cp38.conda#ea6b353536f42246cd130c7fef1285cf
+https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-h4a8ded7_14.conda#f6c14886b1695a2462d296176e831080
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
+https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_14.conda#d5f7a1cca06f56e6ac2b525f199f9b9e
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
 https://conda.anaconda.org/conda-forge/linux-64/coreutils-9.5-hd590300_0.conda#126d457e0e7a535278e808a7d8960015
@@ -24,30 +26,30 @@ https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30
 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
+https://conda.anaconda.org/bioconda/linux-64/k8-1.0-h6618dc6_0.tar.bz2#b43ec67ac9997bfe775cbba4780214af
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
 https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a
 https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.3-h2797004_0.conda#b3316cbe90249da4f8e84cd66e1cc55b
 https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
-https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.6-h232c23b_2.conda#9a3a42df8a95f65334dfc7b80da1195d
+https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.7-hc051c1a_0.conda#5d801a4906adc712d480afc362623b59
 https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda#f2cfec9406850991f4e3d960cc9e3321
 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
 https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
-https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
-https://conda.anaconda.org/bioconda/linux-64/k8-0.2.5-hdcf5f25_4.tar.bz2#d3c49a96ae45864706037702775ca7c2
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
-https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h2fb2949_1000.conda#7e3726e647a619c6ce5939014dfde86d
-https://conda.anaconda.org/conda-forge/linux-64/python-3.10.14-hd12c33a_0_cpython.conda#2b4ba962994e8bd4be9ff5b64b75aff2
+https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h5622ce7_1001.conda#fc2d5b79c2d3f8568fbab31db7ae02f3
+https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_1.tar.bz2#6d03bc0121ddd6e2f8321fa010418eb0
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.19-hd12c33a_0_cpython.conda#53aabe8cf596487ec6f1ce319c93a741
 https://conda.anaconda.org/bioconda/linux-64/hisat2-2.2.1-hdbdd923_6.tar.bz2#98bb9f67fee33c105f41a9f86c3f8c23
-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.7.1-hca28451_0.conda#755c7f876815003337d2c61ff5d047e5
-https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_0.tar.bz2#27d83cfe6bca3eb50aaeb6334371122d
-https://conda.anaconda.org/conda-forge/noarch/setuptools-69.5.1-pyhd8ed1ab_0.conda#7462280d81f639363e6e63c81276bd9e
-https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h00ab1b0_0.conda#f1b776cff1b426e7e7461a8502a3b731
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_0.conda#f21c27f076a07907e70c49bb57bd0f20
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda#c8ddb4f34a208df4dd42509a0f6a1c89
+https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h297d8ca_1.conda#3ff978d8994f591818a506640c6a7071
 https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae
-https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.3-py310ha0a81b8_1.tar.bz2#a9f05707d3225f1d14f613b0064d1eea
+https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.4-he20e202_0.tar.bz2#c9e131332789019b1b70018011f82035
 https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h81da01d_0.tar.bz2#1084947eefd2bbe9c1f84ca24061a9d5
 https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67
 https://conda.anaconda.org/bioconda/linux-64/samtools-1.20-h50ea8bc_0.tar.bz2#7b3b1d0feea64e7e211ae24e7cd126d8
diff --git a/bio/bismark/bam2nuc/environment.yaml b/bio/bismark/bam2nuc/environment.yaml
index 414ff2c472f..959da2ddfa8 100644
--- a/bio/bismark/bam2nuc/environment.yaml
+++ b/bio/bismark/bam2nuc/environment.yaml
@@ -3,6 +3,6 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bowtie2 =2.5.3
+  - bowtie2 =2.5.4
   - bismark =0.24.2
   - samtools =1.20

From 1b232d24816a40f75568bec224eff4e164b3f953 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 24 May 2024 01:33:20 +0000
Subject: [PATCH 04/41] perf: autobump
 bio/bismark/bismark_methylation_extractor (#2944)

Automatic bump of bio/bismark/bismark_methylation_extractor.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 .../environment.linux-64.pin.txt              | 44 ++++++++++---------
 .../environment.yaml                          |  2 +-
 2 files changed, 24 insertions(+), 22 deletions(-)

diff --git a/bio/bismark/bismark_methylation_extractor/environment.linux-64.pin.txt b/bio/bismark/bismark_methylation_extractor/environment.linux-64.pin.txt
index 7d3622852d9..ff0068c3b8a 100644
--- a/bio/bismark/bismark_methylation_extractor/environment.linux-64.pin.txt
+++ b/bio/bismark/bismark_methylation_extractor/environment.linux-64.pin.txt
@@ -3,20 +3,22 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_14.conda#38d211c448a67f12fe693fe25df4da23
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
 https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45
 https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6
 https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb
-https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_1.conda#6185f640c43843e5ad6fd1c5372c3f80
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
-https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce
-https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda#10569984e7db886e4f1abc2b47ad79a1
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-4_cp38.conda#ea6b353536f42246cd130c7fef1285cf
 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-h4a8ded7_14.conda#f6c14886b1695a2462d296176e831080
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
+https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_14.conda#d5f7a1cca06f56e6ac2b525f199f9b9e
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
 https://conda.anaconda.org/conda-forge/linux-64/coreutils-9.5-hd590300_0.conda#126d457e0e7a535278e808a7d8960015
@@ -32,39 +34,39 @@ https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-hd590300_2.conda#d
 https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.0.0-hd590300_1.conda#ea25936bb4080d843790b586850f82b8
 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7
 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
-https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.3.2-hd590300_1.conda#049b7df8bae5e184d1de42cdf64855f8
+https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.4.0-hd590300_0.conda#b26e8aa824079e1be0294e7152ca4559
 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
 https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.2-h59595ed_0.conda#53fb86322bdb89496d7579fe3f02fd61
+https://conda.anaconda.org/bioconda/linux-64/k8-1.0-h6618dc6_0.tar.bz2#b43ec67ac9997bfe775cbba4780214af
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
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-https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.6-h232c23b_2.conda#9a3a42df8a95f65334dfc7b80da1195d
+https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.7-hc051c1a_0.conda#5d801a4906adc712d480afc362623b59
 https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda#f2cfec9406850991f4e3d960cc9e3321
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-https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
 https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb
-https://conda.anaconda.org/bioconda/linux-64/k8-0.2.5-hdcf5f25_4.tar.bz2#d3c49a96ae45864706037702775ca7c2
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
-https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h2fb2949_1000.conda#7e3726e647a619c6ce5939014dfde86d
+https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h5622ce7_1001.conda#fc2d5b79c2d3f8568fbab31db7ae02f3
 https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h1dd3fc0_3.conda#66f03896ffbe1a110ffda05c7a856504
-https://conda.anaconda.org/conda-forge/linux-64/python-3.10.14-hd12c33a_0_cpython.conda#2b4ba962994e8bd4be9ff5b64b75aff2
+https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_1.tar.bz2#6d03bc0121ddd6e2f8321fa010418eb0
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.19-hd12c33a_0_cpython.conda#53aabe8cf596487ec6f1ce319c93a741
 https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.14.2-h14ed4e7_0.conda#0f69b688f52ff6da70bccb7ff7001d1d
 https://conda.anaconda.org/bioconda/linux-64/hisat2-2.2.1-hdbdd923_6.tar.bz2#98bb9f67fee33c105f41a9f86c3f8c23
-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.7.1-hca28451_0.conda#755c7f876815003337d2c61ff5d047e5
-https://conda.anaconda.org/conda-forge/linux-64/libwebp-1.3.2-h658648e_1.conda#0ebb65e8d86843865796c7c95a941f34
-https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_0.tar.bz2#27d83cfe6bca3eb50aaeb6334371122d
-https://conda.anaconda.org/conda-forge/noarch/setuptools-69.5.1-pyhd8ed1ab_0.conda#7462280d81f639363e6e63c81276bd9e
-https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h00ab1b0_0.conda#f1b776cff1b426e7e7461a8502a3b731
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_0.conda#f21c27f076a07907e70c49bb57bd0f20
+https://conda.anaconda.org/conda-forge/linux-64/libwebp-1.4.0-h2c329e2_0.conda#80030debaa84cfc31755d53742df3ca6
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda#c8ddb4f34a208df4dd42509a0f6a1c89
+https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h297d8ca_1.conda#3ff978d8994f591818a506640c6a7071
 https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae
-https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.3-py310ha0a81b8_1.tar.bz2#a9f05707d3225f1d14f613b0064d1eea
+https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.4-he20e202_0.tar.bz2#c9e131332789019b1b70018011f82035
 https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h81da01d_0.tar.bz2#1084947eefd2bbe9c1f84ca24061a9d5
 https://conda.anaconda.org/conda-forge/linux-64/libgd-2.3.3-h119a65a_9.conda#cfebc557e54905dadc355c0e9f003004
 https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67
diff --git a/bio/bismark/bismark_methylation_extractor/environment.yaml b/bio/bismark/bismark_methylation_extractor/environment.yaml
index 8a72197d806..1e170f8774e 100644
--- a/bio/bismark/bismark_methylation_extractor/environment.yaml
+++ b/bio/bismark/bismark_methylation_extractor/environment.yaml
@@ -3,7 +3,7 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bowtie2 =2.5.3
+  - bowtie2 =2.5.4
   - bismark =0.24.2
   - samtools =1.20
   - perl-gdgraph =1.54

From 899ae0d96d04fa56a7ba5989d9dea18be0d3ebc6 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 24 May 2024 01:34:26 +0000
Subject: [PATCH 05/41] perf: autobump bio/bismark/bismark_genome_preparation
 (#2945)

Automatic bump of bio/bismark/bismark_genome_preparation.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 .../environment.linux-64.pin.txt              | 38 ++++++++++---------
 .../environment.yaml                          |  2 +-
 2 files changed, 21 insertions(+), 19 deletions(-)

diff --git a/bio/bismark/bismark_genome_preparation/environment.linux-64.pin.txt b/bio/bismark/bismark_genome_preparation/environment.linux-64.pin.txt
index 904bacb38de..24fb8348f53 100644
--- a/bio/bismark/bismark_genome_preparation/environment.linux-64.pin.txt
+++ b/bio/bismark/bismark_genome_preparation/environment.linux-64.pin.txt
@@ -3,14 +3,16 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_14.conda#38d211c448a67f12fe693fe25df4da23
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
-https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce
-https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda#10569984e7db886e4f1abc2b47ad79a1
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-4_cp38.conda#ea6b353536f42246cd130c7fef1285cf
+https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-h4a8ded7_14.conda#f6c14886b1695a2462d296176e831080
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
+https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_14.conda#d5f7a1cca06f56e6ac2b525f199f9b9e
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
 https://conda.anaconda.org/conda-forge/linux-64/coreutils-9.5-hd590300_0.conda#126d457e0e7a535278e808a7d8960015
@@ -24,30 +26,30 @@ https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30
 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
+https://conda.anaconda.org/bioconda/linux-64/k8-1.0-h6618dc6_0.tar.bz2#b43ec67ac9997bfe775cbba4780214af
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
 https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a
 https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.3-h2797004_0.conda#b3316cbe90249da4f8e84cd66e1cc55b
 https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
-https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.6-h232c23b_2.conda#9a3a42df8a95f65334dfc7b80da1195d
+https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.7-hc051c1a_0.conda#5d801a4906adc712d480afc362623b59
 https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda#f2cfec9406850991f4e3d960cc9e3321
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 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
 https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
-https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
-https://conda.anaconda.org/bioconda/linux-64/k8-0.2.5-hdcf5f25_4.tar.bz2#d3c49a96ae45864706037702775ca7c2
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
-https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h2fb2949_1000.conda#7e3726e647a619c6ce5939014dfde86d
-https://conda.anaconda.org/conda-forge/linux-64/python-3.10.14-hd12c33a_0_cpython.conda#2b4ba962994e8bd4be9ff5b64b75aff2
+https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h5622ce7_1001.conda#fc2d5b79c2d3f8568fbab31db7ae02f3
+https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_1.tar.bz2#6d03bc0121ddd6e2f8321fa010418eb0
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.19-hd12c33a_0_cpython.conda#53aabe8cf596487ec6f1ce319c93a741
 https://conda.anaconda.org/bioconda/linux-64/hisat2-2.2.1-hdbdd923_6.tar.bz2#98bb9f67fee33c105f41a9f86c3f8c23
-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.7.1-hca28451_0.conda#755c7f876815003337d2c61ff5d047e5
-https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_0.tar.bz2#27d83cfe6bca3eb50aaeb6334371122d
-https://conda.anaconda.org/conda-forge/noarch/setuptools-69.5.1-pyhd8ed1ab_0.conda#7462280d81f639363e6e63c81276bd9e
-https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h00ab1b0_0.conda#f1b776cff1b426e7e7461a8502a3b731
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_0.conda#f21c27f076a07907e70c49bb57bd0f20
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda#c8ddb4f34a208df4dd42509a0f6a1c89
+https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h297d8ca_1.conda#3ff978d8994f591818a506640c6a7071
 https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae
-https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.3-py310ha0a81b8_1.tar.bz2#a9f05707d3225f1d14f613b0064d1eea
+https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.4-he20e202_0.tar.bz2#c9e131332789019b1b70018011f82035
 https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h81da01d_0.tar.bz2#1084947eefd2bbe9c1f84ca24061a9d5
 https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67
 https://conda.anaconda.org/bioconda/linux-64/samtools-1.20-h50ea8bc_0.tar.bz2#7b3b1d0feea64e7e211ae24e7cd126d8
diff --git a/bio/bismark/bismark_genome_preparation/environment.yaml b/bio/bismark/bismark_genome_preparation/environment.yaml
index 414ff2c472f..959da2ddfa8 100644
--- a/bio/bismark/bismark_genome_preparation/environment.yaml
+++ b/bio/bismark/bismark_genome_preparation/environment.yaml
@@ -3,6 +3,6 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bowtie2 =2.5.3
+  - bowtie2 =2.5.4
   - bismark =0.24.2
   - samtools =1.20

From bfb3d305daa519faee4ad4ea7dbd313941f4c128 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 24 May 2024 01:36:53 +0000
Subject: [PATCH 06/41] perf: autobump bio/bismark/bismark2summary (#2946)

Automatic bump of bio/bismark/bismark2summary.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 .../environment.linux-64.pin.txt              | 38 ++++++++++---------
 bio/bismark/bismark2summary/environment.yaml  |  2 +-
 2 files changed, 21 insertions(+), 19 deletions(-)

diff --git a/bio/bismark/bismark2summary/environment.linux-64.pin.txt b/bio/bismark/bismark2summary/environment.linux-64.pin.txt
index 904bacb38de..24fb8348f53 100644
--- a/bio/bismark/bismark2summary/environment.linux-64.pin.txt
+++ b/bio/bismark/bismark2summary/environment.linux-64.pin.txt
@@ -3,14 +3,16 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_14.conda#38d211c448a67f12fe693fe25df4da23
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
-https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce
-https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda#10569984e7db886e4f1abc2b47ad79a1
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-4_cp38.conda#ea6b353536f42246cd130c7fef1285cf
+https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-h4a8ded7_14.conda#f6c14886b1695a2462d296176e831080
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
+https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_14.conda#d5f7a1cca06f56e6ac2b525f199f9b9e
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
 https://conda.anaconda.org/conda-forge/linux-64/coreutils-9.5-hd590300_0.conda#126d457e0e7a535278e808a7d8960015
@@ -24,30 +26,30 @@ https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30
 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
+https://conda.anaconda.org/bioconda/linux-64/k8-1.0-h6618dc6_0.tar.bz2#b43ec67ac9997bfe775cbba4780214af
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
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-https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.6-h232c23b_2.conda#9a3a42df8a95f65334dfc7b80da1195d
+https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.7-hc051c1a_0.conda#5d801a4906adc712d480afc362623b59
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-https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
-https://conda.anaconda.org/bioconda/linux-64/k8-0.2.5-hdcf5f25_4.tar.bz2#d3c49a96ae45864706037702775ca7c2
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
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-https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h2fb2949_1000.conda#7e3726e647a619c6ce5939014dfde86d
-https://conda.anaconda.org/conda-forge/linux-64/python-3.10.14-hd12c33a_0_cpython.conda#2b4ba962994e8bd4be9ff5b64b75aff2
+https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h5622ce7_1001.conda#fc2d5b79c2d3f8568fbab31db7ae02f3
+https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_1.tar.bz2#6d03bc0121ddd6e2f8321fa010418eb0
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.19-hd12c33a_0_cpython.conda#53aabe8cf596487ec6f1ce319c93a741
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-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.7.1-hca28451_0.conda#755c7f876815003337d2c61ff5d047e5
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+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_0.conda#f21c27f076a07907e70c49bb57bd0f20
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda#c8ddb4f34a208df4dd42509a0f6a1c89
+https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h297d8ca_1.conda#3ff978d8994f591818a506640c6a7071
 https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae
-https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.3-py310ha0a81b8_1.tar.bz2#a9f05707d3225f1d14f613b0064d1eea
+https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.4-he20e202_0.tar.bz2#c9e131332789019b1b70018011f82035
 https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h81da01d_0.tar.bz2#1084947eefd2bbe9c1f84ca24061a9d5
 https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67
 https://conda.anaconda.org/bioconda/linux-64/samtools-1.20-h50ea8bc_0.tar.bz2#7b3b1d0feea64e7e211ae24e7cd126d8
diff --git a/bio/bismark/bismark2summary/environment.yaml b/bio/bismark/bismark2summary/environment.yaml
index 414ff2c472f..959da2ddfa8 100644
--- a/bio/bismark/bismark2summary/environment.yaml
+++ b/bio/bismark/bismark2summary/environment.yaml
@@ -3,6 +3,6 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bowtie2 =2.5.3
+  - bowtie2 =2.5.4
   - bismark =0.24.2
   - samtools =1.20

From ab29098757c3eef17884f198234ec456e19414f9 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 24 May 2024 01:38:32 +0000
Subject: [PATCH 07/41] perf: autobump bio/bismark/bismark2bedGraph (#2947)

Automatic bump of bio/bismark/bismark2bedGraph.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 .../environment.linux-64.pin.txt              | 38 ++++++++++---------
 bio/bismark/bismark2bedGraph/environment.yaml |  2 +-
 2 files changed, 21 insertions(+), 19 deletions(-)

diff --git a/bio/bismark/bismark2bedGraph/environment.linux-64.pin.txt b/bio/bismark/bismark2bedGraph/environment.linux-64.pin.txt
index 904bacb38de..24fb8348f53 100644
--- a/bio/bismark/bismark2bedGraph/environment.linux-64.pin.txt
+++ b/bio/bismark/bismark2bedGraph/environment.linux-64.pin.txt
@@ -3,14 +3,16 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_14.conda#38d211c448a67f12fe693fe25df4da23
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
-https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce
-https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda#10569984e7db886e4f1abc2b47ad79a1
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-4_cp38.conda#ea6b353536f42246cd130c7fef1285cf
+https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-h4a8ded7_14.conda#f6c14886b1695a2462d296176e831080
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
+https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_14.conda#d5f7a1cca06f56e6ac2b525f199f9b9e
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
 https://conda.anaconda.org/conda-forge/linux-64/coreutils-9.5-hd590300_0.conda#126d457e0e7a535278e808a7d8960015
@@ -24,30 +26,30 @@ https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30
 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
+https://conda.anaconda.org/bioconda/linux-64/k8-1.0-h6618dc6_0.tar.bz2#b43ec67ac9997bfe775cbba4780214af
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
 https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a
 https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.3-h2797004_0.conda#b3316cbe90249da4f8e84cd66e1cc55b
 https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
-https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.6-h232c23b_2.conda#9a3a42df8a95f65334dfc7b80da1195d
+https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.7-hc051c1a_0.conda#5d801a4906adc712d480afc362623b59
 https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda#f2cfec9406850991f4e3d960cc9e3321
 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
 https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
-https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
-https://conda.anaconda.org/bioconda/linux-64/k8-0.2.5-hdcf5f25_4.tar.bz2#d3c49a96ae45864706037702775ca7c2
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
-https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h2fb2949_1000.conda#7e3726e647a619c6ce5939014dfde86d
-https://conda.anaconda.org/conda-forge/linux-64/python-3.10.14-hd12c33a_0_cpython.conda#2b4ba962994e8bd4be9ff5b64b75aff2
+https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h5622ce7_1001.conda#fc2d5b79c2d3f8568fbab31db7ae02f3
+https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_1.tar.bz2#6d03bc0121ddd6e2f8321fa010418eb0
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.19-hd12c33a_0_cpython.conda#53aabe8cf596487ec6f1ce319c93a741
 https://conda.anaconda.org/bioconda/linux-64/hisat2-2.2.1-hdbdd923_6.tar.bz2#98bb9f67fee33c105f41a9f86c3f8c23
-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.7.1-hca28451_0.conda#755c7f876815003337d2c61ff5d047e5
-https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_0.tar.bz2#27d83cfe6bca3eb50aaeb6334371122d
-https://conda.anaconda.org/conda-forge/noarch/setuptools-69.5.1-pyhd8ed1ab_0.conda#7462280d81f639363e6e63c81276bd9e
-https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h00ab1b0_0.conda#f1b776cff1b426e7e7461a8502a3b731
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_0.conda#f21c27f076a07907e70c49bb57bd0f20
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda#c8ddb4f34a208df4dd42509a0f6a1c89
+https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h297d8ca_1.conda#3ff978d8994f591818a506640c6a7071
 https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae
-https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.3-py310ha0a81b8_1.tar.bz2#a9f05707d3225f1d14f613b0064d1eea
+https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.4-he20e202_0.tar.bz2#c9e131332789019b1b70018011f82035
 https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h81da01d_0.tar.bz2#1084947eefd2bbe9c1f84ca24061a9d5
 https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67
 https://conda.anaconda.org/bioconda/linux-64/samtools-1.20-h50ea8bc_0.tar.bz2#7b3b1d0feea64e7e211ae24e7cd126d8
diff --git a/bio/bismark/bismark2bedGraph/environment.yaml b/bio/bismark/bismark2bedGraph/environment.yaml
index 414ff2c472f..959da2ddfa8 100644
--- a/bio/bismark/bismark2bedGraph/environment.yaml
+++ b/bio/bismark/bismark2bedGraph/environment.yaml
@@ -3,6 +3,6 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bowtie2 =2.5.3
+  - bowtie2 =2.5.4
   - bismark =0.24.2
   - samtools =1.20

From d9abb20e0e002d9ec16507d86211b0555a2546ba Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 24 May 2024 01:39:42 +0000
Subject: [PATCH 08/41] perf: autobump bio/bismark/bismark (#2948)

Automatic bump of bio/bismark/bismark.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 .../bismark/environment.linux-64.pin.txt      | 38 ++++++++++---------
 bio/bismark/bismark/environment.yaml          |  2 +-
 2 files changed, 21 insertions(+), 19 deletions(-)

diff --git a/bio/bismark/bismark/environment.linux-64.pin.txt b/bio/bismark/bismark/environment.linux-64.pin.txt
index 904bacb38de..24fb8348f53 100644
--- a/bio/bismark/bismark/environment.linux-64.pin.txt
+++ b/bio/bismark/bismark/environment.linux-64.pin.txt
@@ -3,14 +3,16 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_14.conda#38d211c448a67f12fe693fe25df4da23
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
-https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce
-https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda#10569984e7db886e4f1abc2b47ad79a1
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-4_cp38.conda#ea6b353536f42246cd130c7fef1285cf
+https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-h4a8ded7_14.conda#f6c14886b1695a2462d296176e831080
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
+https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_14.conda#d5f7a1cca06f56e6ac2b525f199f9b9e
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
 https://conda.anaconda.org/conda-forge/linux-64/coreutils-9.5-hd590300_0.conda#126d457e0e7a535278e808a7d8960015
@@ -24,30 +26,30 @@ https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30
 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
+https://conda.anaconda.org/bioconda/linux-64/k8-1.0-h6618dc6_0.tar.bz2#b43ec67ac9997bfe775cbba4780214af
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
 https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a
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 https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
-https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.6-h232c23b_2.conda#9a3a42df8a95f65334dfc7b80da1195d
+https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.7-hc051c1a_0.conda#5d801a4906adc712d480afc362623b59
 https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda#f2cfec9406850991f4e3d960cc9e3321
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 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
 https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
-https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
-https://conda.anaconda.org/bioconda/linux-64/k8-0.2.5-hdcf5f25_4.tar.bz2#d3c49a96ae45864706037702775ca7c2
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
-https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h2fb2949_1000.conda#7e3726e647a619c6ce5939014dfde86d
-https://conda.anaconda.org/conda-forge/linux-64/python-3.10.14-hd12c33a_0_cpython.conda#2b4ba962994e8bd4be9ff5b64b75aff2
+https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h5622ce7_1001.conda#fc2d5b79c2d3f8568fbab31db7ae02f3
+https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_1.tar.bz2#6d03bc0121ddd6e2f8321fa010418eb0
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.19-hd12c33a_0_cpython.conda#53aabe8cf596487ec6f1ce319c93a741
 https://conda.anaconda.org/bioconda/linux-64/hisat2-2.2.1-hdbdd923_6.tar.bz2#98bb9f67fee33c105f41a9f86c3f8c23
-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.7.1-hca28451_0.conda#755c7f876815003337d2c61ff5d047e5
-https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_0.tar.bz2#27d83cfe6bca3eb50aaeb6334371122d
-https://conda.anaconda.org/conda-forge/noarch/setuptools-69.5.1-pyhd8ed1ab_0.conda#7462280d81f639363e6e63c81276bd9e
-https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h00ab1b0_0.conda#f1b776cff1b426e7e7461a8502a3b731
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_0.conda#f21c27f076a07907e70c49bb57bd0f20
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda#c8ddb4f34a208df4dd42509a0f6a1c89
+https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h297d8ca_1.conda#3ff978d8994f591818a506640c6a7071
 https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae
-https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.3-py310ha0a81b8_1.tar.bz2#a9f05707d3225f1d14f613b0064d1eea
+https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.4-he20e202_0.tar.bz2#c9e131332789019b1b70018011f82035
 https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h81da01d_0.tar.bz2#1084947eefd2bbe9c1f84ca24061a9d5
 https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67
 https://conda.anaconda.org/bioconda/linux-64/samtools-1.20-h50ea8bc_0.tar.bz2#7b3b1d0feea64e7e211ae24e7cd126d8
diff --git a/bio/bismark/bismark/environment.yaml b/bio/bismark/bismark/environment.yaml
index 414ff2c472f..959da2ddfa8 100644
--- a/bio/bismark/bismark/environment.yaml
+++ b/bio/bismark/bismark/environment.yaml
@@ -3,6 +3,6 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bowtie2 =2.5.3
+  - bowtie2 =2.5.4
   - bismark =0.24.2
   - samtools =1.20

From 6b0593facfcae0b9c92cb1f31423426752c0230d Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 24 May 2024 01:41:33 +0000
Subject: [PATCH 09/41] perf: autobump bio/bowtie2/align (#2949)

Automatic bump of bio/bowtie2/align.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 .../align/environment.linux-64.pin.txt        | 31 +++++++++----------
 bio/bowtie2/align/environment.yaml            |  2 +-
 2 files changed, 16 insertions(+), 17 deletions(-)

diff --git a/bio/bowtie2/align/environment.linux-64.pin.txt b/bio/bowtie2/align/environment.linux-64.pin.txt
index 60de4162565..f894df9ea5d 100644
--- a/bio/bowtie2/align/environment.linux-64.pin.txt
+++ b/bio/bowtie2/align/environment.linux-64.pin.txt
@@ -4,47 +4,46 @@
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
-https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda#10569984e7db886e4f1abc2b47ad79a1
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
 https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
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 https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda#cc47e1facc155f91abd89b11e48e72ff
 https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
 https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda#8e88f9389f1165d7c0936fe40d9a9a79
 https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
+https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d
 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
 https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-hd590300_2.conda#d66573916ffcf376178462f1b61c941e
 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7
 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
 https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a
 https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.3-h2797004_0.conda#b3316cbe90249da4f8e84cd66e1cc55b
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-https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.6-h232c23b_2.conda#9a3a42df8a95f65334dfc7b80da1195d
+https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.7-hc051c1a_0.conda#5d801a4906adc712d480afc362623b59
 https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda#f2cfec9406850991f4e3d960cc9e3321
 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
-https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
-https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
-https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h2fb2949_1000.conda#7e3726e647a619c6ce5939014dfde86d
-https://conda.anaconda.org/conda-forge/linux-64/python-3.10.14-hd12c33a_0_cpython.conda#2b4ba962994e8bd4be9ff5b64b75aff2
-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.7.1-hca28451_0.conda#755c7f876815003337d2c61ff5d047e5
-https://conda.anaconda.org/conda-forge/noarch/setuptools-69.5.1-pyhd8ed1ab_0.conda#7462280d81f639363e6e63c81276bd9e
+https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h5622ce7_1001.conda#fc2d5b79c2d3f8568fbab31db7ae02f3
+https://conda.anaconda.org/conda-forge/linux-64/python-3.12.3-hab00c5b_0_cpython.conda#2540b74d304f71d3e89c81209db4db84
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_0.conda#f21c27f076a07907e70c49bb57bd0f20
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda#c8ddb4f34a208df4dd42509a0f6a1c89
 https://conda.anaconda.org/bioconda/noarch/snakemake-wrapper-utils-0.6.2-pyhdfd78af_0.tar.bz2#fd8759bbd04116eace828c4fab906096
-https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h00ab1b0_0.conda#f1b776cff1b426e7e7461a8502a3b731
+https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h297d8ca_1.conda#3ff978d8994f591818a506640c6a7071
 https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae
-https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.3-py310ha0a81b8_1.tar.bz2#a9f05707d3225f1d14f613b0064d1eea
+https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.4-he20e202_0.tar.bz2#c9e131332789019b1b70018011f82035
 https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h81da01d_0.tar.bz2#1084947eefd2bbe9c1f84ca24061a9d5
 https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67
 https://conda.anaconda.org/bioconda/linux-64/samtools-1.20-h50ea8bc_0.tar.bz2#7b3b1d0feea64e7e211ae24e7cd126d8
diff --git a/bio/bowtie2/align/environment.yaml b/bio/bowtie2/align/environment.yaml
index a30af4c7ba6..a0293523b17 100644
--- a/bio/bowtie2/align/environment.yaml
+++ b/bio/bowtie2/align/environment.yaml
@@ -3,6 +3,6 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bowtie2 =2.5.3
+  - bowtie2 =2.5.4
   - samtools =1.20
   - snakemake-wrapper-utils =0.6.2

From bcf3c06887443dae9749254f0e8d34e30f880b7e Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 24 May 2024 01:49:11 +0000
Subject: [PATCH 10/41] perf: autobump bio/bismark/deduplicate_bismark (#2950)

Automatic bump of bio/bismark/deduplicate_bismark.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 .../environment.linux-64.pin.txt              | 38 ++++++++++---------
 .../deduplicate_bismark/environment.yaml      |  2 +-
 2 files changed, 21 insertions(+), 19 deletions(-)

diff --git a/bio/bismark/deduplicate_bismark/environment.linux-64.pin.txt b/bio/bismark/deduplicate_bismark/environment.linux-64.pin.txt
index 904bacb38de..24fb8348f53 100644
--- a/bio/bismark/deduplicate_bismark/environment.linux-64.pin.txt
+++ b/bio/bismark/deduplicate_bismark/environment.linux-64.pin.txt
@@ -3,14 +3,16 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_14.conda#38d211c448a67f12fe693fe25df4da23
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
-https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce
-https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda#10569984e7db886e4f1abc2b47ad79a1
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-4_cp38.conda#ea6b353536f42246cd130c7fef1285cf
+https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-h4a8ded7_14.conda#f6c14886b1695a2462d296176e831080
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
+https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_14.conda#d5f7a1cca06f56e6ac2b525f199f9b9e
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
 https://conda.anaconda.org/conda-forge/linux-64/coreutils-9.5-hd590300_0.conda#126d457e0e7a535278e808a7d8960015
@@ -24,30 +26,30 @@ https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30
 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
+https://conda.anaconda.org/bioconda/linux-64/k8-1.0-h6618dc6_0.tar.bz2#b43ec67ac9997bfe775cbba4780214af
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
 https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a
 https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.3-h2797004_0.conda#b3316cbe90249da4f8e84cd66e1cc55b
 https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
-https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.6-h232c23b_2.conda#9a3a42df8a95f65334dfc7b80da1195d
+https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.7-hc051c1a_0.conda#5d801a4906adc712d480afc362623b59
 https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda#f2cfec9406850991f4e3d960cc9e3321
 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
 https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
-https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
-https://conda.anaconda.org/bioconda/linux-64/k8-0.2.5-hdcf5f25_4.tar.bz2#d3c49a96ae45864706037702775ca7c2
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
-https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h2fb2949_1000.conda#7e3726e647a619c6ce5939014dfde86d
-https://conda.anaconda.org/conda-forge/linux-64/python-3.10.14-hd12c33a_0_cpython.conda#2b4ba962994e8bd4be9ff5b64b75aff2
+https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h5622ce7_1001.conda#fc2d5b79c2d3f8568fbab31db7ae02f3
+https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_1.tar.bz2#6d03bc0121ddd6e2f8321fa010418eb0
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.19-hd12c33a_0_cpython.conda#53aabe8cf596487ec6f1ce319c93a741
 https://conda.anaconda.org/bioconda/linux-64/hisat2-2.2.1-hdbdd923_6.tar.bz2#98bb9f67fee33c105f41a9f86c3f8c23
-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.7.1-hca28451_0.conda#755c7f876815003337d2c61ff5d047e5
-https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_0.tar.bz2#27d83cfe6bca3eb50aaeb6334371122d
-https://conda.anaconda.org/conda-forge/noarch/setuptools-69.5.1-pyhd8ed1ab_0.conda#7462280d81f639363e6e63c81276bd9e
-https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h00ab1b0_0.conda#f1b776cff1b426e7e7461a8502a3b731
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_0.conda#f21c27f076a07907e70c49bb57bd0f20
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda#c8ddb4f34a208df4dd42509a0f6a1c89
+https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h297d8ca_1.conda#3ff978d8994f591818a506640c6a7071
 https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae
-https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.3-py310ha0a81b8_1.tar.bz2#a9f05707d3225f1d14f613b0064d1eea
+https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.4-he20e202_0.tar.bz2#c9e131332789019b1b70018011f82035
 https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h81da01d_0.tar.bz2#1084947eefd2bbe9c1f84ca24061a9d5
 https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67
 https://conda.anaconda.org/bioconda/linux-64/samtools-1.20-h50ea8bc_0.tar.bz2#7b3b1d0feea64e7e211ae24e7cd126d8
diff --git a/bio/bismark/deduplicate_bismark/environment.yaml b/bio/bismark/deduplicate_bismark/environment.yaml
index 0207c634d19..96f9fea4f8c 100644
--- a/bio/bismark/deduplicate_bismark/environment.yaml
+++ b/bio/bismark/deduplicate_bismark/environment.yaml
@@ -4,5 +4,5 @@ channels:
   - nodefaults
 dependencies:
   - bismark =0.24.2
-  - bowtie2 =2.5.3
+  - bowtie2 =2.5.4
   - samtools =1.20

From 13dd155a20025b8aaaa80ce3747e6822562bb6b1 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 24 May 2024 01:52:27 +0000
Subject: [PATCH 11/41] perf: autobump bio/bismark/bismark2report (#2951)

Automatic bump of bio/bismark/bismark2report.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 .../environment.linux-64.pin.txt              | 38 ++++++++++---------
 bio/bismark/bismark2report/environment.yaml   |  2 +-
 2 files changed, 21 insertions(+), 19 deletions(-)

diff --git a/bio/bismark/bismark2report/environment.linux-64.pin.txt b/bio/bismark/bismark2report/environment.linux-64.pin.txt
index 904bacb38de..24fb8348f53 100644
--- a/bio/bismark/bismark2report/environment.linux-64.pin.txt
+++ b/bio/bismark/bismark2report/environment.linux-64.pin.txt
@@ -3,14 +3,16 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_14.conda#38d211c448a67f12fe693fe25df4da23
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
-https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce
-https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda#10569984e7db886e4f1abc2b47ad79a1
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-4_cp38.conda#ea6b353536f42246cd130c7fef1285cf
+https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-h4a8ded7_14.conda#f6c14886b1695a2462d296176e831080
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
+https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_14.conda#d5f7a1cca06f56e6ac2b525f199f9b9e
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
 https://conda.anaconda.org/conda-forge/linux-64/coreutils-9.5-hd590300_0.conda#126d457e0e7a535278e808a7d8960015
@@ -24,30 +26,30 @@ https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30
 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
+https://conda.anaconda.org/bioconda/linux-64/k8-1.0-h6618dc6_0.tar.bz2#b43ec67ac9997bfe775cbba4780214af
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
 https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a
 https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.3-h2797004_0.conda#b3316cbe90249da4f8e84cd66e1cc55b
 https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
-https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.6-h232c23b_2.conda#9a3a42df8a95f65334dfc7b80da1195d
+https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.7-hc051c1a_0.conda#5d801a4906adc712d480afc362623b59
 https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda#f2cfec9406850991f4e3d960cc9e3321
 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
 https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
-https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
-https://conda.anaconda.org/bioconda/linux-64/k8-0.2.5-hdcf5f25_4.tar.bz2#d3c49a96ae45864706037702775ca7c2
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
-https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h2fb2949_1000.conda#7e3726e647a619c6ce5939014dfde86d
-https://conda.anaconda.org/conda-forge/linux-64/python-3.10.14-hd12c33a_0_cpython.conda#2b4ba962994e8bd4be9ff5b64b75aff2
+https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h5622ce7_1001.conda#fc2d5b79c2d3f8568fbab31db7ae02f3
+https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_1.tar.bz2#6d03bc0121ddd6e2f8321fa010418eb0
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.19-hd12c33a_0_cpython.conda#53aabe8cf596487ec6f1ce319c93a741
 https://conda.anaconda.org/bioconda/linux-64/hisat2-2.2.1-hdbdd923_6.tar.bz2#98bb9f67fee33c105f41a9f86c3f8c23
-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.7.1-hca28451_0.conda#755c7f876815003337d2c61ff5d047e5
-https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_0.tar.bz2#27d83cfe6bca3eb50aaeb6334371122d
-https://conda.anaconda.org/conda-forge/noarch/setuptools-69.5.1-pyhd8ed1ab_0.conda#7462280d81f639363e6e63c81276bd9e
-https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h00ab1b0_0.conda#f1b776cff1b426e7e7461a8502a3b731
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_0.conda#f21c27f076a07907e70c49bb57bd0f20
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda#c8ddb4f34a208df4dd42509a0f6a1c89
+https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h297d8ca_1.conda#3ff978d8994f591818a506640c6a7071
 https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae
-https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.3-py310ha0a81b8_1.tar.bz2#a9f05707d3225f1d14f613b0064d1eea
+https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.4-he20e202_0.tar.bz2#c9e131332789019b1b70018011f82035
 https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h81da01d_0.tar.bz2#1084947eefd2bbe9c1f84ca24061a9d5
 https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67
 https://conda.anaconda.org/bioconda/linux-64/samtools-1.20-h50ea8bc_0.tar.bz2#7b3b1d0feea64e7e211ae24e7cd126d8
diff --git a/bio/bismark/bismark2report/environment.yaml b/bio/bismark/bismark2report/environment.yaml
index 414ff2c472f..959da2ddfa8 100644
--- a/bio/bismark/bismark2report/environment.yaml
+++ b/bio/bismark/bismark2report/environment.yaml
@@ -3,6 +3,6 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bowtie2 =2.5.3
+  - bowtie2 =2.5.4
   - bismark =0.24.2
   - samtools =1.20

From e45fcac221ef45f345a516bff905a53c864e7355 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 24 May 2024 03:02:47 +0000
Subject: [PATCH 12/41] perf: autobump bio/fastq_screen (#2952)

Automatic bump of bio/fastq_screen.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 bio/fastq_screen/environment.linux-64.pin.txt | 56 +++++++++----------
 bio/fastq_screen/environment.yaml             |  2 +-
 2 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/bio/fastq_screen/environment.linux-64.pin.txt b/bio/fastq_screen/environment.linux-64.pin.txt
index baf105b9a2d..bf09b86b4e1 100644
--- a/bio/fastq_screen/environment.linux-64.pin.txt
+++ b/bio/fastq_screen/environment.linux-64.pin.txt
@@ -3,59 +3,59 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.11.17-hbcca054_0.conda#01ffc8d36f9eba0ce0b3c1955fa780ee
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
 https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45
 https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6
 https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb
-https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_1.conda#6185f640c43843e5ad6fd1c5372c3f80
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_3.conda#937eaed008f6bf2191c5fe76f87755e9
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda#10569984e7db886e4f1abc2b47ad79a1
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
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diff --git a/bio/fastq_screen/environment.yaml b/bio/fastq_screen/environment.yaml
index f8cbf648544..e2cd8805114 100644
--- a/bio/fastq_screen/environment.yaml
+++ b/bio/fastq_screen/environment.yaml
@@ -4,5 +4,5 @@ channels:
   - nodefaults
 dependencies:
   - fastq-screen =0.15.3
-  - bowtie2 =2.5.3
+  - bowtie2 =2.5.4
   - bowtie =1.3.1

From dda3d16c9b49145bd58d287db1021c41d5a24710 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 24 May 2024 03:16:34 +0000
Subject: [PATCH 13/41] perf: autobump bio/gseapy/gsea (#2953)

Automatic bump of bio/gseapy/gsea.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 bio/gseapy/gsea/environment.linux-64.pin.txt | 60 ++++++++++----------
 bio/gseapy/gsea/environment.yaml             |  2 +-
 2 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/bio/gseapy/gsea/environment.linux-64.pin.txt b/bio/gseapy/gsea/environment.linux-64.pin.txt
index cdf2dc51107..d187c6c3e29 100644
--- a/bio/gseapy/gsea/environment.linux-64.pin.txt
+++ b/bio/gseapy/gsea/environment.linux-64.pin.txt
@@ -4,77 +4,77 @@
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+https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-22_linux64_openblas.conda#1a2a0cd3153464fee6646f3dd6dad9b8
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-https://conda.anaconda.org/conda-forge/noarch/setuptools-69.1.1-pyhd8ed1ab_0.conda#576de899521b7d43674ba3ef6eae9142
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda#c8ddb4f34a208df4dd42509a0f6a1c89
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-https://conda.anaconda.org/conda-forge/noarch/wheel-0.42.0-pyhd8ed1ab_0.conda#1cdea58981c5cbc17b51973bcaddcea7
-https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.49.0-py310h2372a71_0.conda#e61ae80fde506b70a88e5e06376d2068
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-https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-21_linux64_openblas.conda#1a42f305615c3867684e049e85927531
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-https://conda.anaconda.org/conda-forge/noarch/requests-2.31.0-pyhd8ed1ab_0.conda#a30144e4156cdbb236f99ebb49828f8b
-https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.2.0-py310hd41b1e2_0.conda#85d2aaa7af046528d339da1e813c3a9f
-https://conda.anaconda.org/conda-forge/linux-64/pandas-2.2.1-py310hcc13569_0.conda#cf5d315e3601a6a2931f63aa9a84dc40
-https://conda.anaconda.org/conda-forge/linux-64/scipy-1.12.0-py310hb13e2d6_2.conda#cd3baec470071490bc5ab05da64c52b5
-https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.8.3-py310h62c0568_0.conda#4a7296c0273eb01dfbed728dd6a6725a
-https://conda.anaconda.org/bioconda/linux-64/gseapy-1.1.2-py310hbee2dd9_0.tar.bz2#b21fd867014e089991d79bf8842dba8d
+https://conda.anaconda.org/conda-forge/noarch/requests-2.32.2-pyhd8ed1ab_0.conda#e1643b34b19df8c028a4f00bf5df58a6
+https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.2.1-py310hd41b1e2_0.conda#60ee50b1968f802f2a487ba36d4cce0d
+https://conda.anaconda.org/conda-forge/linux-64/pandas-2.2.2-py310hf9f9076_1.conda#18100768350158f1795ab9ad7d06d5ca
+https://conda.anaconda.org/conda-forge/linux-64/scipy-1.13.1-py310h93e2701_0.conda#9a697144b2f3adc88ada6b6201b379c4
+https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.8.4-py310hef631a5_2.conda#b3fa3fc2a0fa8b53b913c94297b12e27
+https://conda.anaconda.org/bioconda/linux-64/gseapy-1.1.3-py310hbee2dd9_0.tar.bz2#be269ee4d20c46031054db6d502b818e
diff --git a/bio/gseapy/gsea/environment.yaml b/bio/gseapy/gsea/environment.yaml
index 2aac907a928..0c30b760c96 100644
--- a/bio/gseapy/gsea/environment.yaml
+++ b/bio/gseapy/gsea/environment.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - gseapy =1.1.2
+  - gseapy =1.1.3

From 32d25c1560b4c581694c49dc6d3a596e5ca581ab Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 24 May 2024 03:32:48 +0000
Subject: [PATCH 14/41] perf: autobump bio/gdc-api/bam-slicing (#2954)

Automatic bump of bio/gdc-api/bam-slicing.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 .../bam-slicing/environment.linux-64.pin.txt   | 18 +++++++++---------
 bio/gdc-api/bam-slicing/environment.yaml       |  2 +-
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/bio/gdc-api/bam-slicing/environment.linux-64.pin.txt b/bio/gdc-api/bam-slicing/environment.linux-64.pin.txt
index a5ba88331a1..170a097095b 100644
--- a/bio/gdc-api/bam-slicing/environment.linux-64.pin.txt
+++ b/bio/gdc-api/bam-slicing/environment.linux-64.pin.txt
@@ -4,20 +4,20 @@
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
-https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.27.0-hd590300_0.conda#f6afff0e9ee08d2f1b897881a4f38cdb
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
+https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
 https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
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-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
 https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a
 https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
-https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.7.1-hca28451_0.conda#755c7f876815003337d2c61ff5d047e5
-https://conda.anaconda.org/conda-forge/linux-64/curl-8.7.1-hca28451_0.conda#d2dd5466be2ce818f8097847341da63d
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_0.conda#f21c27f076a07907e70c49bb57bd0f20
+https://conda.anaconda.org/conda-forge/linux-64/curl-8.8.0-he654da7_0.conda#042341d8b9ba4ee7f2722b81fae9f0ad
diff --git a/bio/gdc-api/bam-slicing/environment.yaml b/bio/gdc-api/bam-slicing/environment.yaml
index 922ce54f27e..59fd406b09e 100644
--- a/bio/gdc-api/bam-slicing/environment.yaml
+++ b/bio/gdc-api/bam-slicing/environment.yaml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - curl =8.7.1
+  - curl =8.8.0

From 91ad1079fa03b07f8ebb9ebf21fe92d21c8a3c13 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 24 May 2024 04:13:15 +0000
Subject: [PATCH 15/41] perf: autobump bio/multiqc (#2955)

Automatic bump of bio/multiqc.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 bio/multiqc/environment.linux-64.pin.txt | 103 +++++++++++------------
 bio/multiqc/environment.yaml             |   2 +-
 2 files changed, 48 insertions(+), 57 deletions(-)

diff --git a/bio/multiqc/environment.linux-64.pin.txt b/bio/multiqc/environment.linux-64.pin.txt
index 43be7574dae..3dc2bd6ecb3 100644
--- a/bio/multiqc/environment.linux-64.pin.txt
+++ b/bio/multiqc/environment.linux-64.pin.txt
@@ -7,109 +7,100 @@ https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca05
 https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45
 https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6
 https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb
-https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_1.conda#6185f640c43843e5ad6fd1c5372c3f80
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda#10569984e7db886e4f1abc2b47ad79a1
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
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-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
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-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
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-https://conda.anaconda.org/conda-forge/linux-64/libbrotlicommon-1.1.0-hd590300_1.conda#aec6c91c7371c26392a06708a73c70e5
-https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.19-hd590300_0.conda#1635570038840ee3f9c71d22aa5b8b6d
-https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.5.0-hcb278e6_1.conda#6305a3dd2752c76335295da4e581f2fd
+https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda#8e88f9389f1165d7c0936fe40d9a9a79
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-https://conda.anaconda.org/bioconda/noarch/multiqc-1.21-pyhdfd78af_0.tar.bz2#e845de80c3a09438d29802fb9a54a01c
+https://conda.anaconda.org/bioconda/noarch/multiqc-1.22.1-pyhdfd78af_0.tar.bz2#9911803d6b2cea2cc9c45c55debb056f
diff --git a/bio/multiqc/environment.yaml b/bio/multiqc/environment.yaml
index 5153fc3bccf..c15d8d85044 100644
--- a/bio/multiqc/environment.yaml
+++ b/bio/multiqc/environment.yaml
@@ -3,5 +3,5 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - multiqc =1.21
+  - multiqc =1.22.1
   - snakemake-wrapper-utils =0.6.2

From b2a469dc907c8f3761399affd29ca53f012cc3ee Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 24 May 2024 05:10:58 +0000
Subject: [PATCH 16/41] perf: autobump bio/rbt/csvreport (#2956)

Automatic bump of bio/rbt/csvreport.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 .../csvreport/environment.linux-64.pin.txt    | 24 +++++++++----------
 bio/rbt/csvreport/environment.yaml            |  2 +-
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/bio/rbt/csvreport/environment.linux-64.pin.txt b/bio/rbt/csvreport/environment.linux-64.pin.txt
index c47e8b9055f..d378b0fe15b 100644
--- a/bio/rbt/csvreport/environment.linux-64.pin.txt
+++ b/bio/rbt/csvreport/environment.linux-64.pin.txt
@@ -3,17 +3,17 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda#a73ecd2988327ad4c8f2c331482917f2
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda#9172c297304f2a20134fc56c97fbe229
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda#e2042154faafe61969556f28bade94b9
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-ha4646dd_2.conda#78fdab09d9138851dde2b5fe2a11019e
-https://conda.anaconda.org/conda-forge/linux-64/openssl-1.1.1w-hd590300_0.conda#301e70057a3bd399640bb16bbdf87995
-https://conda.anaconda.org/bioconda/linux-64/starcode-1.4-h031d066_4.tar.bz2#ffbbc19f2c42772e60009d821fb1e3f9
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_2.conda#e75a75a6eaf6f318dae2631158c46575
-https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.24-pthreads_h413a1c8_0.conda#6e4ef6ca28655124dcde9bd500e44c32
-https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-19_linux64_openblas.conda#420f4e9be59d0dc9133a0f43f7bab3f3
-https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-19_linux64_openblas.conda#d12374af44575413fbbd4a217d46ea33
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-hca663fb_7.conda#c0bd771f09a326fdcd95a60b617795bf
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c
+https://conda.anaconda.org/bioconda/linux-64/starcode-1.4-h031d066_5.tar.bz2#f1e98071985e015104b9594951055398
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_7.conda#1b84f26d9f4f6026e179e7805d5a15cd
+https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_h413a1c8_0.conda#a356024784da6dfd4683dc5ecf45b155
+https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-22_linux64_openblas.conda#1a2a0cd3153464fee6646f3dd6dad9b8
+https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-22_linux64_openblas.conda#4b31699e0ec5de64d5896e580389c9a1
 https://conda.anaconda.org/conda-forge/linux-64/gsl-2.7-he838d99_0.tar.bz2#fec079ba39c9cca093bf4c00001825de
-https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.42.0-h86f6036_0.tar.bz2#8e0421006219454d4ec66a6adf555160
+https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.42.2-h4458251_1.tar.bz2#3b7cb7a0aab85a1bf374f6a1c390c62c
diff --git a/bio/rbt/csvreport/environment.yaml b/bio/rbt/csvreport/environment.yaml
index c0fbb0dfa56..8803c5347ae 100644
--- a/bio/rbt/csvreport/environment.yaml
+++ b/bio/rbt/csvreport/environment.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - rust-bio-tools =0.42.0
+  - rust-bio-tools =0.42.2

From 185ce7e4bd6adbdf840effa665f62e358865c8b8 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 24 May 2024 05:53:45 +0000
Subject: [PATCH 17/41] perf: autobump bio/unicycler (#2957)

Automatic bump of bio/unicycler.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 bio/unicycler/environment.linux-64.pin.txt | 42 +++++++++++-----------
 bio/unicycler/environment.yaml             |  2 +-
 2 files changed, 22 insertions(+), 22 deletions(-)

diff --git a/bio/unicycler/environment.linux-64.pin.txt b/bio/unicycler/environment.linux-64.pin.txt
index fec35ee25de..b130fb74a39 100644
--- a/bio/unicycler/environment.linux-64.pin.txt
+++ b/bio/unicycler/environment.linux-64.pin.txt
@@ -8,18 +8,18 @@ https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca05
 https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45
 https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6
 https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb
-https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_1.conda#6185f640c43843e5ad6fd1c5372c3f80
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda#10569984e7db886e4f1abc2b47ad79a1
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce
 https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29
 https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-h4a8ded7_14.conda#f6c14886b1695a2462d296176e831080
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab
 https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_14.conda#d5f7a1cca06f56e6ac2b525f199f9b9e
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
 https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.11-hd590300_1.conda#0bb492cca54017ea314b809b1ee3a176
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
@@ -35,7 +35,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172b
 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d
 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
 https://conda.anaconda.org/conda-forge/linux-64/libgettextpo-0.22.5-h59595ed_2.conda#172bcc51059416e7ce99e7b528cede83
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-ha4646dd_5.conda#7a6bd7a12a4bd359e2afe6c0fa1acace
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-hca663fb_7.conda#c0bd771f09a326fdcd95a60b617795bf
 https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-hd590300_2.conda#d66573916ffcf376178462f1b61c941e
 https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.0.0-hd590300_1.conda#ea25936bb4080d843790b586850f82b8
 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7
@@ -45,9 +45,9 @@ https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.4.0-hd590300_0.co
 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
 https://conda.anaconda.org/conda-forge/linux-64/llvm-openmp-8.0.1-hc9558a2_0.tar.bz2#67590caab043d6d7ffc371f9cced7848
-https://conda.anaconda.org/bioconda/linux-64/ncbi-vdb-3.1.0-h4ac6f70_2.tar.bz2#76066b4a20b930b78a8a39cf5fa7a381
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a
+https://conda.anaconda.org/bioconda/linux-64/ncbi-vdb-3.1.1-h4ac6f70_0.tar.bz2#4cbc542ee7db0710bdf07a4e55f5daaf
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c
 https://conda.anaconda.org/conda-forge/linux-64/pcre-8.45-h9c3ff4c_0.tar.bz2#c05d1820a6d34ff07aaaab7a9b7eddaa
 https://conda.anaconda.org/conda-forge/linux-64/pixman-0.43.2-h59595ed_0.conda#71004cbf7924e19c02746ccde9fd7123
 https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2#22dad4df6e8630e8dff2428f6f6a7036
@@ -65,13 +65,13 @@ https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.2-h59595ed_0.conda#53f
 https://conda.anaconda.org/conda-forge/linux-64/libasprintf-devel-0.22.5-h661eb56_2.conda#02e41ab5834dcdcc8590cf29d9526f50
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
 https://conda.anaconda.org/conda-forge/linux-64/libgettextpo-devel-0.22.5-h59595ed_2.conda#b63d9b6da3653179a278077f0de20014
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_5.conda#e73e9cfd1191783392131e6238bdb3e9
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_7.conda#1b84f26d9f4f6026e179e7805d5a15cd
 https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a
 https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.43-h2797004_0.conda#009981dd9cfcaa4dbfa25ffaed86bcae
 https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.3-h2797004_0.conda#b3316cbe90249da4f8e84cd66e1cc55b
 https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
 https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.15-h0b41bf4_0.conda#33277193f5b92bad9fdd230eb700929c
-https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.6-h232c23b_2.conda#9a3a42df8a95f65334dfc7b80da1195d
+https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.7-hc051c1a_0.conda#5d801a4906adc712d480afc362623b59
 https://conda.anaconda.org/conda-forge/linux-64/openmp-8.0.1-0.tar.bz2#b35241079152e5cc891c99368395b2c6
 https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.43-hcad00b1_0.conda#8292dea9e022d9610a11fce5e0896ed8
 https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda#f2cfec9406850991f4e3d960cc9e3321
@@ -80,12 +80,12 @@ https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.con
 https://conda.anaconda.org/conda-forge/linux-64/xorg-fixesproto-5.0-h7f98852_1002.tar.bz2#65ad6e1eb4aed2b0611855aff05e04f6
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libsm-1.2.4-h7391055_0.conda#93ee23f12bc2e684548181256edd2cf6
 https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
-https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
 https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb
 https://conda.anaconda.org/conda-forge/linux-64/gettext-0.22.5-h59595ed_2.conda#219ba82e95d7614cf7140d2a4afc0926
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
-https://conda.anaconda.org/conda-forge/linux-64/libglib-2.80.0-hf2295e7_5.conda#4423ae9726113b68e9527b27baae191f
-https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h2fb2949_1000.conda#7e3726e647a619c6ce5939014dfde86d
+https://conda.anaconda.org/conda-forge/linux-64/libglib-2.80.2-hf974151_0.conda#72724f6a78ecb15559396966226d5838
+https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h5622ce7_1001.conda#fc2d5b79c2d3f8568fbab31db7ae02f3
 https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_h413a1c8_0.conda#a356024784da6dfd4683dc5ecf45b155
 https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h1dd3fc0_3.conda#66f03896ffbe1a110ffda05c7a856504
 https://conda.anaconda.org/bioconda/linux-64/miniasm-0.3-he4a0461_3.tar.bz2#48b210aced98d578b8153ed997a7b69c
@@ -106,24 +106,24 @@ https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.14.2-h14ed4e7_0.con
 https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.16-hb7c19ff_0.conda#51bb7010fc86f70eee639b4bb7a894f5
 https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-22_linux64_openblas.conda#1a2a0cd3153464fee6646f3dd6dad9b8
 https://conda.anaconda.org/conda-forge/linux-64/libcups-2.3.3-h4637d8d_4.conda#d4529f4dff3057982a7617c7ac58fde3
-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.7.1-hca28451_0.conda#755c7f876815003337d2c61ff5d047e5
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_0.conda#f21c27f076a07907e70c49bb57bd0f20
 https://conda.anaconda.org/conda-forge/linux-64/libidn2-2.3.7-hd590300_0.conda#2b7b0d827c6447cc1d85dc06d5b5de46
 https://conda.anaconda.org/conda-forge/noarch/perl-carp-1.50-pl5321hd8ed1ab_0.tar.bz2#bdddc03e28019b902da71b722f2288d7
 https://conda.anaconda.org/conda-forge/linux-64/perl-encode-3.21-pl5321hd590300_0.conda#704fb52dc57c97cf5adcc057c8b40a0a
 https://conda.anaconda.org/bioconda/noarch/perl-list-moreutils-0.430-pl5321hdfd78af_0.tar.bz2#7f04c79d216d0f8e7b6d5a51de4aafa0
 https://conda.anaconda.org/bioconda/noarch/perl-types-serialiser-1.01-pl5321hdfd78af_0.tar.bz2#cfc65753e827bbef80c00eaa395f6ae7
 https://conda.anaconda.org/bioconda/linux-64/racon-1.5.0-h21ec9f0_3.tar.bz2#d481c4b1f6892989583c7ee5535c623c
-https://conda.anaconda.org/conda-forge/noarch/setuptools-69.5.1-pyhd8ed1ab_0.conda#7462280d81f639363e6e63c81276bd9e
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda#c8ddb4f34a208df4dd42509a0f6a1c89
 https://conda.anaconda.org/bioconda/linux-64/spades-3.15.5-h95f258a_1.tar.bz2#62ab35497479905dce6860525262104f
-https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h00ab1b0_0.conda#f1b776cff1b426e7e7461a8502a3b731
+https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h297d8ca_1.conda#3ff978d8994f591818a506640c6a7071
 https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.4-h0b41bf4_2.conda#82b6df12252e6f32402b96dacc656fec
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxfixes-5.0.3-h7f98852_1004.tar.bz2#e9a21aa4d5e3e5f1aed71e8cefd46b6a
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.11-hd590300_0.conda#ed67c36f215b310412b2af935bf3e530
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxt-1.3.0-hd590300_1.conda#ae92aab42726eb29d16488924f7312cb
-https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.3-py310ha0a81b8_1.tar.bz2#a9f05707d3225f1d14f613b0064d1eea
+https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.4-he20e202_0.tar.bz2#c9e131332789019b1b70018011f82035
 https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-h3faef2a_0.conda#f907bb958910dc404647326ca80c263e
-https://conda.anaconda.org/conda-forge/linux-64/curl-8.7.1-hca28451_0.conda#d2dd5466be2ce818f8097847341da63d
+https://conda.anaconda.org/conda-forge/linux-64/curl-8.8.0-he654da7_0.conda#042341d8b9ba4ee7f2722b81fae9f0ad
 https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h81da01d_0.tar.bz2#1084947eefd2bbe9c1f84ca24061a9d5
 https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-22_linux64_openblas.conda#4b31699e0ec5de64d5896e580389c9a1
 https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.201-pl5321hdbdd923_2.tar.bz2#f40f599ce37ad75715bab686baa08197
@@ -134,13 +134,13 @@ https://conda.anaconda.org/conda-forge/linux-64/wget-1.21.4-hda4d442_0.conda#361
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxi-1.7.10-h7f98852_0.tar.bz2#e77615e5141cad5a2acaa043d1cf0ca5
 https://conda.anaconda.org/bioconda/linux-64/entrez-direct-21.6-he881be0_0.tar.bz2#eb24d0563146f7f6419e092526147d06
 https://conda.anaconda.org/conda-forge/linux-64/gsl-2.7-he838d99_0.tar.bz2#fec079ba39c9cca093bf4c00001825de
-https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-8.3.0-h3d44ed6_0.conda#5a6f6c00ef982a9bc83558d9ac8f64a0
+https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-8.5.0-hfac3d4d_0.conda#f5126317dd0ce0ba26945e411ecc6960
 https://conda.anaconda.org/bioconda/noarch/perl-archive-tar-2.40-pl5321hdfd78af_0.tar.bz2#ef5f007762b5ad9425694104d7db4463
 https://conda.anaconda.org/bioconda/noarch/perl-json-4.10-pl5321hdfd78af_0.tar.bz2#05467eeb1e57206d8dddf31c3128cd00
 https://conda.anaconda.org/bioconda/linux-64/samtools-1.20-h50ea8bc_0.tar.bz2#7b3b1d0feea64e7e211ae24e7cd126d8
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxtst-1.2.3-h7f98852_1002.tar.bz2#a220b1a513e19d5cb56c1311d44f12e6
 https://conda.anaconda.org/bioconda/linux-64/bcftools-1.20-h8b25389_0.tar.bz2#227ba3d820ac2f171b2ee20eb780cbac
 https://conda.anaconda.org/bioconda/linux-64/blast-2.15.0-pl5321h6f7f691_1.tar.bz2#f7e6a87317b5d00469d39a2d1ef2698f
-https://conda.anaconda.org/conda-forge/linux-64/openjdk-21.0.3-hb622114_0.conda#35d2887347424180f602682a893a322b
+https://conda.anaconda.org/conda-forge/linux-64/openjdk-22.0.1-hb622114_0.conda#cddebf320a874489f4e231b45e66c1e1
 https://conda.anaconda.org/bioconda/noarch/pilon-1.24-hdfd78af_0.tar.bz2#4eef0c771dd3f81effb0d21ba8bb6734
 https://conda.anaconda.org/bioconda/linux-64/unicycler-0.5.0-py310h6cc9453_3.tar.bz2#a581959132eb2ff31ddd65d15a8349e8
diff --git a/bio/unicycler/environment.yaml b/bio/unicycler/environment.yaml
index 95253aa91c2..8dcf2070a81 100644
--- a/bio/unicycler/environment.yaml
+++ b/bio/unicycler/environment.yaml
@@ -3,7 +3,7 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bowtie2 =2.5.3
+  - bowtie2 =2.5.4
   - bcftools =1.20
   - spades =3.15.5
   - samtools =1.20

From 728658d5fae40ea784f7b8d3c567c4f7240ef7c7 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 24 May 2024 06:03:05 +0000
Subject: [PATCH 18/41] perf: autobump bio/vep/annotate (#2958)

Automatic bump of bio/vep/annotate.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 bio/vep/annotate/environment.linux-64.pin.txt | 32 +++++++++----------
 bio/vep/annotate/environment.yaml             |  2 +-
 2 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/bio/vep/annotate/environment.linux-64.pin.txt b/bio/vep/annotate/environment.linux-64.pin.txt
index c068b99fbb6..9df96ea2285 100644
--- a/bio/vep/annotate/environment.linux-64.pin.txt
+++ b/bio/vep/annotate/environment.linux-64.pin.txt
@@ -9,16 +9,16 @@ https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-2.6.32-he0
 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.39-hcc3a1bd_1.conda#737be0d34c22d24432049ab7a3214de4
 https://conda.anaconda.org/conda-forge/linux-64/libgcc-devel_linux-64-10.4.0-hd38fd1e_19.tar.bz2#b41d6540a78ba2518655eebcb0e41e20
 https://conda.anaconda.org/conda-forge/linux-64/libgfortran-3.0.0-1.tar.bz2#d7c7e92a8ccc518709474dd3eda896b9
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce
 https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.12-he073ed8_17.conda#595db67e32b276298ff3d94d07d47fbf
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
 https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.39-he00db2b_1.conda#3d726e8b51a1f5bfd66892a2b7d9db2d
 https://conda.anaconda.org/conda-forge/linux-64/binutils_linux-64-2.39-h5fc0e48_13.conda#7f25a524665e4e2f8a5f86522f8d0e31
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
-https://conda.anaconda.org/conda-forge/linux-64/argtable2-2.13-h14c3975_1001.tar.bz2#b9e0ac5d747ceab0c8b85a470358e1a6
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
+https://conda.anaconda.org/conda-forge/linux-64/argtable2-2.13-hd590300_1004.conda#d7d089e975b1213c2a0f94e592b7b422
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
 https://conda.anaconda.org/bioconda/linux-64/clustalw-2.1-h4ac6f70_10.tar.bz2#e7756d46d67ea32f90b684f6770f290d
@@ -32,7 +32,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172b
 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d
 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
 https://conda.anaconda.org/conda-forge/linux-64/libgettextpo-0.22.5-h59595ed_2.conda#172bcc51059416e7ce99e7b528cede83
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-ha4646dd_5.conda#7a6bd7a12a4bd359e2afe6c0fa1acace
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-hca663fb_7.conda#c0bd771f09a326fdcd95a60b617795bf
 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7
 https://conda.anaconda.org/conda-forge/linux-64/libsanitizer-10.4.0-h5246dfb_19.tar.bz2#b068ad132a509367bc9e5a200a639429
 https://conda.anaconda.org/conda-forge/linux-64/libunistring-0.9.10-h7f98852_0.tar.bz2#7245a044b4a1980ed83196176b78b73a
@@ -40,21 +40,21 @@ https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#
 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
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 https://conda.anaconda.org/bioconda/linux-64/muscle-5.1-h4ac6f70_3.tar.bz2#aea487cbcbed07625e0963472c4ac568
-https://conda.anaconda.org/bioconda/linux-64/ncbi-vdb-3.1.0-h4ac6f70_2.tar.bz2#76066b4a20b930b78a8a39cf5fa7a381
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a
+https://conda.anaconda.org/bioconda/linux-64/ncbi-vdb-3.1.1-h4ac6f70_0.tar.bz2#4cbc542ee7db0710bdf07a4e55f5daaf
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c
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 https://conda.anaconda.org/bioconda/linux-64/poa-2.0-h031d066_5.tar.bz2#7f92f2dd187e08868ffc6a9e12525f75
 https://conda.anaconda.org/conda-forge/linux-64/unzip-6.0-h7f98852_3.tar.bz2#7cb7109505433a5abbf68bb34b31edac
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
-https://conda.anaconda.org/bioconda/linux-64/clustalo-1.2.4-hdbdd923_7.tar.bz2#24fd3aaebe5ab116cb8fbddd34d62e39
+https://conda.anaconda.org/bioconda/linux-64/clustalo-1.2.4-hdbdd923_8.tar.bz2#9baa8c81d5ca18a5336fe748bfa8e7a9
 https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.2-h59595ed_0.conda#53fb86322bdb89496d7579fe3f02fd61
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 https://conda.anaconda.org/conda-forge/linux-64/libgettextpo-devel-0.22.5-h59595ed_2.conda#b63d9b6da3653179a278077f0de20014
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_5.conda#e73e9cfd1191783392131e6238bdb3e9
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_7.conda#1b84f26d9f4f6026e179e7805d5a15cd
 https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a
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 https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
@@ -64,7 +64,7 @@ https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.con
 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
 https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
-https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
 https://conda.anaconda.org/conda-forge/linux-64/gcc_linux-64-10.4.0-h9215b83_13.conda#a38a8d1059689117691fb736215a196a
 https://conda.anaconda.org/conda-forge/linux-64/gettext-0.22.5-h59595ed_2.conda#219ba82e95d7614cf7140d2a4afc0926
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
@@ -118,7 +118,7 @@ https://conda.anaconda.org/bioconda/noarch/perl-xml-xpathengine-0.14-pl5321hdfd7
 https://conda.anaconda.org/conda-forge/linux-64/python-3.10.14-hd12c33a_0_cpython.conda#2b4ba962994e8bd4be9ff5b64b75aff2
 https://conda.anaconda.org/conda-forge/linux-64/gawk-5.3.0-ha916aea_0.conda#66ef869337c8061f6a96b0348d138a62
 https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-22_linux64_openblas.conda#1a2a0cd3153464fee6646f3dd6dad9b8
-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.7.1-hca28451_0.conda#755c7f876815003337d2c61ff5d047e5
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_0.conda#f21c27f076a07907e70c49bb57bd0f20
 https://conda.anaconda.org/conda-forge/linux-64/libidn2-2.3.7-hd590300_0.conda#2b7b0d827c6447cc1d85dc06d5b5de46
 https://conda.anaconda.org/bioconda/noarch/perl-bioperl-core-1.7.8-pl5321hdfd78af_1.tar.bz2#e627a38fe206468089dc73a0aafb6c8c
 https://conda.anaconda.org/conda-forge/noarch/perl-carp-1.50-pl5321hd8ed1ab_0.tar.bz2#bdddc03e28019b902da71b722f2288d7
@@ -139,13 +139,13 @@ https://conda.anaconda.org/conda-forge/noarch/perl-text-csv-2.02-pl5321hd8ed1ab_
 https://conda.anaconda.org/conda-forge/noarch/perl-text-diff-1.45-pl5321hd8ed1ab_0.tar.bz2#7c91b422ca8ccb679449d1e3cdd3b7d7
 https://conda.anaconda.org/bioconda/noarch/perl-tree-dag_node-1.32-pl5321hdfd78af_0.tar.bz2#09b05f575f3ae5f4a87003c857e3ad5d
 https://conda.anaconda.org/bioconda/noarch/perl-types-serialiser-1.01-pl5321hdfd78af_0.tar.bz2#cfc65753e827bbef80c00eaa395f6ae7
-https://conda.anaconda.org/conda-forge/noarch/setuptools-69.5.1-pyhd8ed1ab_0.conda#7462280d81f639363e6e63c81276bd9e
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda#c8ddb4f34a208df4dd42509a0f6a1c89
 https://conda.anaconda.org/bioconda/linux-64/viennarna-2.6.4-py310pl5321h6cc9453_1.tar.bz2#18fb36de80fd0f7bf4fde40e2eb9dd70
 https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae
-https://conda.anaconda.org/conda-forge/linux-64/curl-8.7.1-hca28451_0.conda#d2dd5466be2ce818f8097847341da63d
+https://conda.anaconda.org/conda-forge/linux-64/curl-8.8.0-he654da7_0.conda#042341d8b9ba4ee7f2722b81fae9f0ad
 https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h81da01d_0.tar.bz2#1084947eefd2bbe9c1f84ca24061a9d5
 https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-22_linux64_openblas.conda#4b31699e0ec5de64d5896e580389c9a1
-https://conda.anaconda.org/conda-forge/linux-64/mafft-7.525-h56fdecd_0.conda#164fe6657ea34e923fe893d5116f3ad5
+https://conda.anaconda.org/conda-forge/linux-64/mafft-7.526-h4ab18f5_0.conda#49583145deca5984ca37c494b06ab7ac
 https://conda.anaconda.org/bioconda/linux-64/perl-bio-samtools-1.43-pl5321he4a0461_4.tar.bz2#e766315d6c69e23e74e5917f77d96ab1
 https://conda.anaconda.org/bioconda/noarch/perl-bio-searchio-hmmer-1.7.3-pl5321hdfd78af_0.tar.bz2#8251ea4d5dc4fd65272ac6700c1d8a21
 https://conda.anaconda.org/conda-forge/noarch/perl-business-isbn-data-20210112.006-pl5321hd8ed1ab_0.tar.bz2#a70f08650ec3919ee5e599834f1349d3
@@ -191,4 +191,4 @@ https://conda.anaconda.org/bioconda/noarch/perl-xml-dom-xpath-0.14-pl5321hdfd78a
 https://conda.anaconda.org/bioconda/noarch/perl-bio-featureio-1.6.905-pl5321hdfd78af_4.tar.bz2#1b4b260b45e9cac33fcb45918cda428b
 https://conda.anaconda.org/bioconda/noarch/perl-bioperl-1.7.8-hdfd78af_1.tar.bz2#a693939710e572d0f85f6058b534e319
 https://conda.anaconda.org/bioconda/linux-64/perl-bio-db-hts-3.01-pl5321h6141fd1_8.tar.bz2#9bd60dd669288d8b6fbcc06dd6c8f3e5
-https://conda.anaconda.org/bioconda/noarch/ensembl-vep-111.0-pl5321h2a3209d_0.tar.bz2#18a2cedc60ea453a12006ca10aac9a61
+https://conda.anaconda.org/bioconda/noarch/ensembl-vep-112.0-pl5321h2a3209d_0.tar.bz2#483c04201882a9ba1b18ddb505ea284b
diff --git a/bio/vep/annotate/environment.yaml b/bio/vep/annotate/environment.yaml
index 5a49f8568bb..98137690f9c 100644
--- a/bio/vep/annotate/environment.yaml
+++ b/bio/vep/annotate/environment.yaml
@@ -3,7 +3,7 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - ensembl-vep =111.0
+  - ensembl-vep =112.0
   - bcftools =1.20
   - perl-encode-locale =1.05
   - perl =5.32.1

From f4e5b66f8765d09d51d4a640d2d775d781c3018f Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 24 May 2024 06:06:00 +0000
Subject: [PATCH 19/41] perf: autobump bio/vep/cache (#2959)

Automatic bump of bio/vep/cache.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 bio/vep/cache/environment.linux-64.pin.txt | 28 +++++++++++-----------
 bio/vep/cache/environment.yaml             |  2 +-
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/bio/vep/cache/environment.linux-64.pin.txt b/bio/vep/cache/environment.linux-64.pin.txt
index 8a6bd533c15..30bb176ba9a 100644
--- a/bio/vep/cache/environment.linux-64.pin.txt
+++ b/bio/vep/cache/environment.linux-64.pin.txt
@@ -9,15 +9,15 @@ https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-2.6.32-he0
 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.39-hcc3a1bd_1.conda#737be0d34c22d24432049ab7a3214de4
 https://conda.anaconda.org/conda-forge/linux-64/libgcc-devel_linux-64-10.4.0-hd38fd1e_19.tar.bz2#b41d6540a78ba2518655eebcb0e41e20
 https://conda.anaconda.org/conda-forge/linux-64/libgfortran-3.0.0-1.tar.bz2#d7c7e92a8ccc518709474dd3eda896b9
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
 https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.12-he073ed8_17.conda#595db67e32b276298ff3d94d07d47fbf
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
 https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.39-he00db2b_1.conda#3d726e8b51a1f5bfd66892a2b7d9db2d
 https://conda.anaconda.org/conda-forge/linux-64/binutils_linux-64-2.39-h5fc0e48_13.conda#7f25a524665e4e2f8a5f86522f8d0e31
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
-https://conda.anaconda.org/conda-forge/linux-64/argtable2-2.13-h14c3975_1001.tar.bz2#b9e0ac5d747ceab0c8b85a470358e1a6
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
+https://conda.anaconda.org/conda-forge/linux-64/argtable2-2.13-hd590300_1004.conda#d7d089e975b1213c2a0f94e592b7b422
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
 https://conda.anaconda.org/bioconda/linux-64/clustalw-2.1-h4ac6f70_10.tar.bz2#e7756d46d67ea32f90b684f6770f290d
@@ -39,15 +39,15 @@ https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#
 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
 https://conda.anaconda.org/bioconda/linux-64/muscle-5.1-h4ac6f70_3.tar.bz2#aea487cbcbed07625e0963472c4ac568
-https://conda.anaconda.org/bioconda/linux-64/ncbi-vdb-3.1.0-h4ac6f70_2.tar.bz2#76066b4a20b930b78a8a39cf5fa7a381
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a
+https://conda.anaconda.org/bioconda/linux-64/ncbi-vdb-3.1.1-h4ac6f70_0.tar.bz2#4cbc542ee7db0710bdf07a4e55f5daaf
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c
 https://conda.anaconda.org/bioconda/linux-64/paml-4.10.7-h031d066_1.tar.bz2#627002991a379d013307808bf9b71676
 https://conda.anaconda.org/conda-forge/linux-64/pcre-8.45-h9c3ff4c_0.tar.bz2#c05d1820a6d34ff07aaaab7a9b7eddaa
 https://conda.anaconda.org/bioconda/linux-64/poa-2.0-h031d066_5.tar.bz2#7f92f2dd187e08868ffc6a9e12525f75
 https://conda.anaconda.org/conda-forge/linux-64/unzip-6.0-h7f98852_3.tar.bz2#7cb7109505433a5abbf68bb34b31edac
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
-https://conda.anaconda.org/bioconda/linux-64/clustalo-1.2.4-hdbdd923_7.tar.bz2#24fd3aaebe5ab116cb8fbddd34d62e39
+https://conda.anaconda.org/bioconda/linux-64/clustalo-1.2.4-hdbdd923_8.tar.bz2#9baa8c81d5ca18a5336fe748bfa8e7a9
 https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.2-h59595ed_0.conda#53fb86322bdb89496d7579fe3f02fd61
 https://conda.anaconda.org/conda-forge/linux-64/gcc_impl_linux-64-10.4.0-h5231bdf_19.tar.bz2#a086547de4cee874e72d5a43230372ec
 https://conda.anaconda.org/conda-forge/linux-64/libasprintf-devel-0.22.5-h661eb56_2.conda#02e41ab5834dcdcc8590cf29d9526f50
@@ -63,7 +63,7 @@ https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47
 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
 https://conda.anaconda.org/bioconda/linux-64/viennarna-2.4.7-py27_2.tar.bz2#7e533112461dea3391f2246460277ea5
 https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
-https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
 https://conda.anaconda.org/conda-forge/linux-64/gcc_linux-64-10.4.0-h9215b83_13.conda#a38a8d1059689117691fb736215a196a
 https://conda.anaconda.org/conda-forge/linux-64/gettext-0.22.5-h59595ed_2.conda#219ba82e95d7614cf7140d2a4afc0926
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
@@ -115,7 +115,7 @@ https://conda.anaconda.org/bioconda/noarch/perl-xml-regexp-0.04-pl5321hdfd78af_3
 https://conda.anaconda.org/bioconda/noarch/perl-xml-xpathengine-0.14-pl5321hdfd78af_3.tar.bz2#4af616066d02762108e88cf5413d3ded
 https://conda.anaconda.org/conda-forge/linux-64/python-3.12.3-hab00c5b_0_cpython.conda#2540b74d304f71d3e89c81209db4db84
 https://conda.anaconda.org/conda-forge/linux-64/gawk-5.3.0-ha916aea_0.conda#66ef869337c8061f6a96b0348d138a62
-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.7.1-hca28451_0.conda#755c7f876815003337d2c61ff5d047e5
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_0.conda#f21c27f076a07907e70c49bb57bd0f20
 https://conda.anaconda.org/conda-forge/linux-64/libidn2-2.3.7-hd590300_0.conda#2b7b0d827c6447cc1d85dc06d5b5de46
 https://conda.anaconda.org/bioconda/noarch/perl-bioperl-core-1.7.8-pl5321hdfd78af_1.tar.bz2#e627a38fe206468089dc73a0aafb6c8c
 https://conda.anaconda.org/conda-forge/noarch/perl-carp-1.50-pl5321hd8ed1ab_0.tar.bz2#bdddc03e28019b902da71b722f2288d7
@@ -136,11 +136,11 @@ https://conda.anaconda.org/conda-forge/noarch/perl-text-csv-2.02-pl5321hd8ed1ab_
 https://conda.anaconda.org/conda-forge/noarch/perl-text-diff-1.45-pl5321hd8ed1ab_0.tar.bz2#7c91b422ca8ccb679449d1e3cdd3b7d7
 https://conda.anaconda.org/bioconda/noarch/perl-tree-dag_node-1.32-pl5321hdfd78af_0.tar.bz2#09b05f575f3ae5f4a87003c857e3ad5d
 https://conda.anaconda.org/bioconda/noarch/perl-types-serialiser-1.01-pl5321hdfd78af_0.tar.bz2#cfc65753e827bbef80c00eaa395f6ae7
-https://conda.anaconda.org/conda-forge/noarch/setuptools-69.5.1-pyhd8ed1ab_0.conda#7462280d81f639363e6e63c81276bd9e
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda#c8ddb4f34a208df4dd42509a0f6a1c89
 https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae
-https://conda.anaconda.org/conda-forge/linux-64/curl-8.7.1-hca28451_0.conda#d2dd5466be2ce818f8097847341da63d
+https://conda.anaconda.org/conda-forge/linux-64/curl-8.8.0-he654da7_0.conda#042341d8b9ba4ee7f2722b81fae9f0ad
 https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h81da01d_0.tar.bz2#1084947eefd2bbe9c1f84ca24061a9d5
-https://conda.anaconda.org/conda-forge/linux-64/mafft-7.525-h56fdecd_0.conda#164fe6657ea34e923fe893d5116f3ad5
+https://conda.anaconda.org/conda-forge/linux-64/mafft-7.526-h4ab18f5_0.conda#49583145deca5984ca37c494b06ab7ac
 https://conda.anaconda.org/bioconda/linux-64/perl-bio-samtools-1.43-pl5321he4a0461_4.tar.bz2#e766315d6c69e23e74e5917f77d96ab1
 https://conda.anaconda.org/bioconda/noarch/perl-bio-searchio-hmmer-1.7.3-pl5321hdfd78af_0.tar.bz2#8251ea4d5dc4fd65272ac6700c1d8a21
 https://conda.anaconda.org/conda-forge/noarch/perl-business-isbn-data-20210112.006-pl5321hd8ed1ab_0.tar.bz2#a70f08650ec3919ee5e599834f1349d3
@@ -184,4 +184,4 @@ https://conda.anaconda.org/bioconda/noarch/perl-xml-dom-xpath-0.14-pl5321hdfd78a
 https://conda.anaconda.org/bioconda/noarch/perl-bio-featureio-1.6.905-pl5321hdfd78af_4.tar.bz2#1b4b260b45e9cac33fcb45918cda428b
 https://conda.anaconda.org/bioconda/noarch/perl-bioperl-1.7.8-hdfd78af_1.tar.bz2#a693939710e572d0f85f6058b534e319
 https://conda.anaconda.org/bioconda/linux-64/perl-bio-db-hts-3.01-pl5321h6141fd1_8.tar.bz2#9bd60dd669288d8b6fbcc06dd6c8f3e5
-https://conda.anaconda.org/bioconda/noarch/ensembl-vep-111.0-pl5321h2a3209d_0.tar.bz2#18a2cedc60ea453a12006ca10aac9a61
+https://conda.anaconda.org/bioconda/noarch/ensembl-vep-112.0-pl5321h2a3209d_0.tar.bz2#483c04201882a9ba1b18ddb505ea284b
diff --git a/bio/vep/cache/environment.yaml b/bio/vep/cache/environment.yaml
index c1a4d1c5525..e5df77fb24b 100644
--- a/bio/vep/cache/environment.yaml
+++ b/bio/vep/cache/environment.yaml
@@ -4,4 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - python =3.12.3
-  - ensembl-vep =111.0
+  - ensembl-vep =112.0

From e10ab571a63b36ce1295e50b6f6b7e4742e0beae Mon Sep 17 00:00:00 2001
From: "Filipe G. Vieira" <1151762+fgvieira@users.noreply.github.com>
Date: Tue, 28 May 2024 14:02:46 +0200
Subject: [PATCH 20/41] fix: issue #366 and #2649 (#2928)

<!-- Ensure that the PR title follows conventional commit style (<type>:
<description>)-->
<!-- Possible types are here:
https://github.com/commitizen/conventional-commit-types/blob/master/index.json
-->

<!-- Add a description of your PR here-->
Allow for custom URLs (fix issues #366 and #2649).

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] I confirm that:

For all wrappers added by this PR,

* there is a test case which covers any introduced changes,
* `input:` and `output:` file paths in the resulting rule can be changed
arbitrarily,
* either the wrapper can only use a single core, or the example rule
contains a `threads: x` statement with `x` being a reasonable default,
* rule names in the test case are in
[snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell
what the rule is about or match the tools purpose or name (e.g.,
`map_reads` for a step that maps reads),
* all `environment.yaml` specifications follow [the respective best
practices](https://stackoverflow.com/a/64594513/2352071),
* the `environment.yaml` pinning has been updated by running
`snakedeploy pin-conda-envs environment.yaml` on a linux machine,
* wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`),
* all fields of the example rules in the `Snakefile`s and their entries
are explained via comments (`input:`/`output:`/`params:` etc.),
* `stderr` and/or `stdout` are logged correctly (`log:`), depending on
the wrapped tool,
* temporary files are either written to a unique hidden folder in the
working directory, or (better) stored where the Python function
`tempfile.gettempdir()` points to (see
[here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir);
this also means that using any Python `tempfile` default behavior
works),
* the `meta.yaml` contains a link to the documentation of the respective
tool or command,
* `Snakefile`s pass the linting (`snakemake --lint`),
* `Snakefile`s are formatted with
[snakefmt](https://github.com/snakemake/snakefmt),
* Python wrapper scripts are formatted with
[black](https://black.readthedocs.io).
* Conda environments use a minimal amount of channels, in recommended
ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as
conda-forge should have highest priority and defaults channels are
usually not needed because most packages are in conda-forge nowadays).
---
 bio/reference/ensembl-annotation/meta.yaml      |  2 ++
 bio/reference/ensembl-annotation/test/Snakefile |  2 ++
 bio/reference/ensembl-annotation/wrapper.py     | 13 ++-----------
 bio/reference/ensembl-sequence/meta.yaml        |  4 ++++
 bio/reference/ensembl-sequence/test/Snakefile   |  2 ++
 bio/reference/ensembl-sequence/wrapper.py       |  3 ++-
 bio/reference/ensembl-variation/meta.yaml       |  4 ++++
 bio/reference/ensembl-variation/test/Snakefile  |  2 ++
 bio/reference/ensembl-variation/wrapper.py      | 10 +++-------
 bio/vep/cache/meta.yaml                         |  7 +++++++
 bio/vep/cache/test/Snakefile                    | 15 +++++++++++++++
 bio/vep/cache/wrapper.py                        | 11 ++++++-----
 test.py                                         |  5 +++++
 13 files changed, 56 insertions(+), 24 deletions(-)

diff --git a/bio/reference/ensembl-annotation/meta.yaml b/bio/reference/ensembl-annotation/meta.yaml
index be0a0bb69be..b8fd0924a79 100644
--- a/bio/reference/ensembl-annotation/meta.yaml
+++ b/bio/reference/ensembl-annotation/meta.yaml
@@ -4,3 +4,5 @@ authors:
   - Johannes Köster
 output:
   - Ensemble GTF or GFF3 anotation file
+params:
+  - url: URL from where to download cache data (optional; by default is ``ftp://ftp.ensembl.org/pub``)
diff --git a/bio/reference/ensembl-annotation/test/Snakefile b/bio/reference/ensembl-annotation/test/Snakefile
index fed87b2ee64..3a30ca70bde 100644
--- a/bio/reference/ensembl-annotation/test/Snakefile
+++ b/bio/reference/ensembl-annotation/test/Snakefile
@@ -25,6 +25,8 @@ rule get_annotation_gz:
         # branch="plants",  # optional: specify branch
     log:
         "logs/get_annotation.log",
+    params:
+        url="http://ftp.ensembl.org/pub",
     cache: "omit-software"  # save space and time with between workflow caching (see docs)
     wrapper:
         "master/bio/reference/ensembl-annotation"
diff --git a/bio/reference/ensembl-annotation/wrapper.py b/bio/reference/ensembl-annotation/wrapper.py
index 2f1b78c2a6a..c3d655cbb25 100644
--- a/bio/reference/ensembl-annotation/wrapper.py
+++ b/bio/reference/ensembl-annotation/wrapper.py
@@ -48,17 +48,8 @@
     )
 
 
-url = "ftp://ftp.ensembl.org/pub/{branch}release-{release}/{out_fmt}/{species}/{species_cap}.{build}.{gtf_release}.{flavor}{suffix}".format(
-    release=release,
-    gtf_release=gtf_release,
-    build=build,
-    species=species,
-    out_fmt=out_fmt,
-    species_cap=species.capitalize(),
-    suffix=suffix,
-    flavor=flavor,
-    branch=branch,
-)
+url = snakemake.params.get("url", "ftp://ftp.ensembl.org/pub")
+url = f"{url}/{branch}release-{release}/{out_fmt}/{species}/{species.capitalize()}.{build}.{gtf_release}.{flavor}{suffix}"
 
 
 try:
diff --git a/bio/reference/ensembl-sequence/meta.yaml b/bio/reference/ensembl-sequence/meta.yaml
index 189912a20e5..20c769a0d1d 100644
--- a/bio/reference/ensembl-sequence/meta.yaml
+++ b/bio/reference/ensembl-sequence/meta.yaml
@@ -2,3 +2,7 @@ name: ensembl-sequence
 description: Download sequences (e.g. genome) from ENSEMBL FTP servers, and store them in a single .fasta file.
 authors:
   - Johannes Köster
+output:
+  - fasta file
+params:
+  - url: URL from where to download cache data (optional; by default is ``ftp://ftp.ensembl.org/pub``)
diff --git a/bio/reference/ensembl-sequence/test/Snakefile b/bio/reference/ensembl-sequence/test/Snakefile
index a8227f4cdd1..fec1c746a4c 100644
--- a/bio/reference/ensembl-sequence/test/Snakefile
+++ b/bio/reference/ensembl-sequence/test/Snakefile
@@ -25,6 +25,8 @@ rule get_single_chromosome:
         # branch="plants",  # optional: specify branch
     log:
         "logs/get_genome.log",
+    params:
+        url="http://ftp.ensembl.org/pub",
     cache: "omit-software"  # save space and time with between workflow caching (see docs)
     wrapper:
         "master/bio/reference/ensembl-sequence"
diff --git a/bio/reference/ensembl-sequence/wrapper.py b/bio/reference/ensembl-sequence/wrapper.py
index df9a6eef693..cb2956a6c04 100644
--- a/bio/reference/ensembl-sequence/wrapper.py
+++ b/bio/reference/ensembl-sequence/wrapper.py
@@ -50,8 +50,9 @@
             "invalid datatype, to select a single chromosome the datatype must be dna"
         )
 
+url = snakemake.params.get("url", "ftp://ftp.ensembl.org/pub")
 spec = spec.format(build=build, release=release)
-url_prefix = f"ftp://ftp.ensembl.org/pub/{branch}release-{release}/fasta/{species}/{datatype}/{species.capitalize()}.{spec}"
+url_prefix = f"{url}/{branch}release-{release}/fasta/{species}/{datatype}/{species.capitalize()}.{spec}"
 
 success = False
 for suffix in suffixes:
diff --git a/bio/reference/ensembl-variation/meta.yaml b/bio/reference/ensembl-variation/meta.yaml
index b562872809c..3f1a261ae4b 100644
--- a/bio/reference/ensembl-variation/meta.yaml
+++ b/bio/reference/ensembl-variation/meta.yaml
@@ -2,3 +2,7 @@ name: ensembl-variation
 description: Download known genomic variants from ENSEMBL FTP servers, and store them in a single .vcf.gz file.
 authors:
   - Johannes Köster
+output:
+  - VCF file
+params:
+  - url: URL from where to download cache data (optional; by default is ``ftp://ftp.ensembl.org/pub``)
diff --git a/bio/reference/ensembl-variation/test/Snakefile b/bio/reference/ensembl-variation/test/Snakefile
index 27594273e57..9189f7de194 100644
--- a/bio/reference/ensembl-variation/test/Snakefile
+++ b/bio/reference/ensembl-variation/test/Snakefile
@@ -12,6 +12,8 @@ rule get_variation:
         type="all",  # one of "all", "somatic", "structural_variation"
         # chromosome="21", # optionally constrain to chromosome, only supported for homo_sapiens
         # branch="plants",  # optional: specify branch
+    params:
+        url="http://ftp.ensembl.org/pub",
     log:
         "logs/get_variation.log",
     cache: "omit-software"  # save space and time with between workflow caching (see docs)
diff --git a/bio/reference/ensembl-variation/wrapper.py b/bio/reference/ensembl-variation/wrapper.py
index ee179c51c1d..4e21292886a 100644
--- a/bio/reference/ensembl-variation/wrapper.py
+++ b/bio/reference/ensembl-variation/wrapper.py
@@ -62,16 +62,12 @@
 
 species_filename = species if release >= 91 else species.capitalize()
 
+url = snakemake.params.get("url", "ftp://ftp.ensembl.org/pub")
 urls = [
-    "ftp://ftp.ensembl.org/pub/{branch}release-{release}/variation/vcf/{species}/{species_filename}{suffix}.vcf.gz".format(
-        release=release,
-        species=species,
-        suffix=suffix,
-        species_filename=species_filename,
-        branch=branch,
-    )
+    f"{url}/{branch}release-{release}/variation/vcf/{species}/{species_filename}{suffix}.vcf.gz"
     for suffix in suffixes
 ]
+
 names = [os.path.basename(url) for url in urls]
 
 try:
diff --git a/bio/vep/cache/meta.yaml b/bio/vep/cache/meta.yaml
index a743fdd138d..220cec2c1f6 100644
--- a/bio/vep/cache/meta.yaml
+++ b/bio/vep/cache/meta.yaml
@@ -3,3 +3,10 @@ description: Download VEP cache for given species, build and release.
 url: http://www.ensembl.org/info/docs/tools/vep/index.html
 authors:
   - Johannes Köster
+output:
+  - directory to store the VEP cache
+params:
+  - url: URL from where to download cache data (optional; by default is ``ftp://ftp.ensembl.org/pub``)
+  - species: species to download cache data
+  - build: build to download cache data
+  - release: release to download cache data
diff --git a/bio/vep/cache/test/Snakefile b/bio/vep/cache/test/Snakefile
index 4f6285893c1..c2666c9547b 100644
--- a/bio/vep/cache/test/Snakefile
+++ b/bio/vep/cache/test/Snakefile
@@ -10,3 +10,18 @@ rule get_vep_cache:
     cache: "omit-software"  # save space and time with between workflow caching (see docs)
     wrapper:
         "master/bio/vep/cache"
+
+
+rule get_vep_cache_ebi:
+    output:
+        directory("resources/vep/cache_ebi"),
+    params:
+        url="ftp://ftp.ebi.ac.uk/ensemblgenomes/pub/plants",
+        species="cyanidioschyzon_merolae",
+        build="ASM9120v1",
+        release="58",
+    log:
+        "logs/vep/cache_ebi.log",
+    cache: "omit-software"  # save space and time with between workflow caching (see docs)
+    wrapper:
+        "master/bio/vep/cache"
diff --git a/bio/vep/cache/wrapper.py b/bio/vep/cache/wrapper.py
index 543f1b26169..291d8161210 100644
--- a/bio/vep/cache/wrapper.py
+++ b/bio/vep/cache/wrapper.py
@@ -9,24 +9,25 @@
 
 
 extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
 
 try:
     release = int(snakemake.params.release)
 except ValueError:
     raise ValueError("The parameter release is supposed to be an integer.")
 
+
 with tempfile.TemporaryDirectory() as tmpdir:
     # We download the cache tarball manually because vep_install does not consider proxy settings (in contrast to curl).
     # See https://github.com/bcbio/bcbio-nextgen/issues/1080
-    vep_dir = "vep" if release >= 97 else "VEP"
+    cache_url = snakemake.params.get("url", "ftp://ftp.ensembl.org/pub")
     cache_tarball = (
         f"{snakemake.params.species}_vep_{release}_{snakemake.params.build}.tar.gz"
     )
-    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+    vep_dir = "vep" if snakemake.params.get("url") or release >= 97 else "VEP"
     shell(
-        "curl -L ftp://ftp.ensembl.org/pub/release-{snakemake.params.release}/"
-        "variation/{vep_dir}/{cache_tarball} "
-        "-o {tmpdir}/{cache_tarball} {log}"
+        "curl -L {cache_url}/release-{release}/variation/{vep_dir}/{cache_tarball} -o {tmpdir}/{cache_tarball} {log}"
     )
 
     log = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True)
diff --git a/test.py b/test.py
index cab6ba917b9..6e8aa7e5fef 100644
--- a/test.py
+++ b/test.py
@@ -5965,6 +5965,11 @@ def test_vep_cache():
         ["snakemake", "--cores", "1", "resources/vep/cache", "--use-conda", "-F"],
     )
 
+    run(
+        "bio/vep/cache",
+        ["snakemake", "--cores", "1", "resources/vep/cache_ebi", "--use-conda", "-F"],
+    )
+
 
 @skip_if_not_modified
 def test_vep_plugins():

From 3c86baef4586b596c6c3375336828257e8bb815f Mon Sep 17 00:00:00 2001
From: "Filipe G. Vieira" <1151762+fgvieira@users.noreply.github.com>
Date: Tue, 28 May 2024 14:03:16 +0200
Subject: [PATCH 21/41] feat: add samtools markdup wrapper (#2926)

<!-- Ensure that the PR title follows conventional commit style (<type>:
<description>)-->
<!-- Possible types are here:
https://github.com/commitizen/conventional-commit-types/blob/master/index.json
-->

<!-- Add a description of your PR here-->

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] I confirm that:

For all wrappers added by this PR,

* there is a test case which covers any introduced changes,
* `input:` and `output:` file paths in the resulting rule can be changed
arbitrarily,
* either the wrapper can only use a single core, or the example rule
contains a `threads: x` statement with `x` being a reasonable default,
* rule names in the test case are in
[snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell
what the rule is about or match the tools purpose or name (e.g.,
`map_reads` for a step that maps reads),
* all `environment.yaml` specifications follow [the respective best
practices](https://stackoverflow.com/a/64594513/2352071),
* the `environment.yaml` pinning has been updated by running
`snakedeploy pin-conda-envs environment.yaml` on a linux machine,
* wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`),
* all fields of the example rules in the `Snakefile`s and their entries
are explained via comments (`input:`/`output:`/`params:` etc.),
* `stderr` and/or `stdout` are logged correctly (`log:`), depending on
the wrapped tool,
* temporary files are either written to a unique hidden folder in the
working directory, or (better) stored where the Python function
`tempfile.gettempdir()` points to (see
[here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir);
this also means that using any Python `tempfile` default behavior
works),
* the `meta.yaml` contains a link to the documentation of the respective
tool or command,
* `Snakefile`s pass the linting (`snakemake --lint`),
* `Snakefile`s are formatted with
[snakefmt](https://github.com/snakemake/snakefmt),
* Python wrapper scripts are formatted with
[black](https://black.readthedocs.io).
* Conda environments use a minimal amount of channels, in recommended
ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as
conda-forge should have highest priority and defaults channels are
usually not needed because most packages are in conda-forge nowadays).

---------

Co-authored-by: Christian Meesters <cmeesters@users.noreply.github.com>
---
 bio/samtools/calmd/meta.yaml                  |  11 +++--
 .../markdup/environment.linux-64.pin.txt      |  42 ++++++++++++++++++
 bio/samtools/markdup/environment.yaml         |   7 +++
 bio/samtools/markdup/meta.yaml                |  12 +++++
 bio/samtools/markdup/test/Snakefile           |  13 ++++++
 bio/samtools/markdup/test/a.bam               | Bin 0 -> 65521 bytes
 bio/samtools/markdup/wrapper.py               |  24 ++++++++++
 test.py                                       |   8 ++++
 8 files changed, 114 insertions(+), 3 deletions(-)
 create mode 100644 bio/samtools/markdup/environment.linux-64.pin.txt
 create mode 100644 bio/samtools/markdup/environment.yaml
 create mode 100644 bio/samtools/markdup/meta.yaml
 create mode 100644 bio/samtools/markdup/test/Snakefile
 create mode 100644 bio/samtools/markdup/test/a.bam
 create mode 100644 bio/samtools/markdup/wrapper.py

diff --git a/bio/samtools/calmd/meta.yaml b/bio/samtools/calmd/meta.yaml
index 120aa104299..b7f708dcc87 100644
--- a/bio/samtools/calmd/meta.yaml
+++ b/bio/samtools/calmd/meta.yaml
@@ -1,7 +1,12 @@
 name: samtools calmd
 description: Calculates MD and NM tags.
+url: http://www.htslib.org/doc/samtools-calmd.html
 authors:
   - Filipe G. Vieira
-notes: |
-  * The `extra` param allows for additional program arguments (not `-@/--threads` or `-O/--output-fmt`).
-  * For more information see, http://www.htslib.org/doc/samtools-calmd.html
+input:
+  - SAM/BAM/CRAM file
+output:
+  - SAM/BAM/CRAM file
+  - SAM/BAM/CRAM index file (optional)
+params:
+  - extra: additional program arguments (not `-@/--threads`, `--write-index`, `-m`, `-o` or `-O/--output-fmt`).
diff --git a/bio/samtools/markdup/environment.linux-64.pin.txt b/bio/samtools/markdup/environment.linux-64.pin.txt
new file mode 100644
index 00000000000..3dde3547a55
--- /dev/null
+++ b/bio/samtools/markdup/environment.linux-64.pin.txt
@@ -0,0 +1,42 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
+https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
+https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
+https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda#8e88f9389f1165d7c0936fe40d9a9a79
+https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
+https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
+https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
+https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.3-h2797004_0.conda#b3316cbe90249da4f8e84cd66e1cc55b
+https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
+https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
+https://conda.anaconda.org/conda-forge/linux-64/python-3.12.3-hab00c5b_0_cpython.conda#2540b74d304f71d3e89c81209db4db84
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.7.1-hca28451_0.conda#755c7f876815003337d2c61ff5d047e5
+https://conda.anaconda.org/conda-forge/noarch/setuptools-69.5.1-pyhd8ed1ab_0.conda#7462280d81f639363e6e63c81276bd9e
+https://conda.anaconda.org/bioconda/noarch/snakemake-wrapper-utils-0.6.2-pyhdfd78af_0.tar.bz2#fd8759bbd04116eace828c4fab906096
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae
+https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h81da01d_0.tar.bz2#1084947eefd2bbe9c1f84ca24061a9d5
+https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67
+https://conda.anaconda.org/bioconda/linux-64/samtools-1.20-h50ea8bc_0.tar.bz2#7b3b1d0feea64e7e211ae24e7cd126d8
diff --git a/bio/samtools/markdup/environment.yaml b/bio/samtools/markdup/environment.yaml
new file mode 100644
index 00000000000..3defe4e72c3
--- /dev/null
+++ b/bio/samtools/markdup/environment.yaml
@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - samtools =1.20
+  - snakemake-wrapper-utils =0.6.2
diff --git a/bio/samtools/markdup/meta.yaml b/bio/samtools/markdup/meta.yaml
new file mode 100644
index 00000000000..8365a417d28
--- /dev/null
+++ b/bio/samtools/markdup/meta.yaml
@@ -0,0 +1,12 @@
+name: samtools markdup
+description: Mark duplicate alignments in a coordinate sorted file .
+url: http://www.htslib.org/doc/samtools-markdup.html
+authors:
+  - Filipe G. Vieira
+input:
+  - SAM/BAM/CRAM file
+output:
+  - SAM/BAM/CRAM file
+  - SAM/BAM/CRAM index file (optional)
+params:
+  - extra: additional program arguments (not `-@/--threads`, `--write-index`, `-m`, `-T`, `-f`, `-o` or `-O/--output-fmt`).
diff --git a/bio/samtools/markdup/test/Snakefile b/bio/samtools/markdup/test/Snakefile
new file mode 100644
index 00000000000..930e352d314
--- /dev/null
+++ b/bio/samtools/markdup/test/Snakefile
@@ -0,0 +1,13 @@
+rule samtools_markdup:
+    input:
+        aln="{sample}.bam",
+    output:
+        bam="{sample}.markdup.bam",
+        idx="{sample}.markdup.bam.csi",
+    log:
+        "{sample}.markdup.log",
+    params:
+        extra="-c --no-PG",
+    threads: 2
+    wrapper:
+        "master/bio/samtools/markdup"
diff --git a/bio/samtools/markdup/test/a.bam b/bio/samtools/markdup/test/a.bam
new file mode 100644
index 0000000000000000000000000000000000000000..622f848271205c370a51e6388d97f77810d65836
GIT binary patch
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diff --git a/bio/samtools/markdup/wrapper.py b/bio/samtools/markdup/wrapper.py
new file mode 100644
index 00000000000..ef6443b8d64
--- /dev/null
+++ b/bio/samtools/markdup/wrapper.py
@@ -0,0 +1,24 @@
+__author__ = "Filipe G. Vieira"
+__copyright__ = "Copyright 2024, Filipe G. Vieira"
+__license__ = "MIT"
+
+
+import tempfile
+from pathlib import Path
+from snakemake.shell import shell
+from snakemake_wrapper_utils.samtools import get_samtools_opts
+
+samtools_opts = get_samtools_opts(snakemake, parse_output=False)
+extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=False, stderr=True)
+
+metrics = snakemake.output.get("metrics", "")
+if metrics:
+    metrics = f"-f {metrics}"
+
+
+with tempfile.TemporaryDirectory() as tmpdir:
+    tmp_prefix = Path(tmpdir) / "samtools_markdup"
+    shell(
+        "samtools markdup {samtools_opts} {extra} -T {tmp_prefix} {metrics} {snakemake.input[0]} {snakemake.output[0]} {log}"
+    )
diff --git a/test.py b/test.py
index 6e8aa7e5fef..df62e06ed0c 100644
--- a/test.py
+++ b/test.py
@@ -4097,6 +4097,14 @@ def test_samtools_mpileup():
     )
 
 
+@skip_if_not_modified
+def test_samtools_mpileup():
+    run(
+        "bio/samtools/markdup",
+        ["snakemake", "--cores", "1", "a.markdup.bam", "--use-conda", "-F"],
+    )
+
+
 @skip_if_not_modified
 def test_samtools_stats():
     run(

From 9c8cf81c1894fc019ffbf0f906eb88e0960c3e7d Mon Sep 17 00:00:00 2001
From: Felix Wiegand <fxwiegand@wgdnet.de>
Date: Tue, 28 May 2024 14:58:14 +0200
Subject: [PATCH 22/41] perf: Use samtools collate in fastq separate wrapper
 (#2960)

<!-- Ensure that the PR title follows conventional commit style (<type>:
<description>)-->
<!-- Possible types are here:
https://github.com/commitizen/conventional-commit-types/blob/master/index.json
-->

<!-- Add a description of your PR here-->

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] I confirm that:

For all wrappers added by this PR,

* there is a test case which covers any introduced changes,
* `input:` and `output:` file paths in the resulting rule can be changed
arbitrarily,
* either the wrapper can only use a single core, or the example rule
contains a `threads: x` statement with `x` being a reasonable default,
* rule names in the test case are in
[snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell
what the rule is about or match the tools purpose or name (e.g.,
`map_reads` for a step that maps reads),
* all `environment.yaml` specifications follow [the respective best
practices](https://stackoverflow.com/a/64594513/2352071),
* the `environment.yaml` pinning has been updated by running
`snakedeploy pin-conda-envs environment.yaml` on a linux machine,
* wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`),
* all fields of the example rules in the `Snakefile`s and their entries
are explained via comments (`input:`/`output:`/`params:` etc.),
* `stderr` and/or `stdout` are logged correctly (`log:`), depending on
the wrapped tool,
* temporary files are either written to a unique hidden folder in the
working directory, or (better) stored where the Python function
`tempfile.gettempdir()` points to (see
[here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir);
this also means that using any Python `tempfile` default behavior
works),
* the `meta.yaml` contains a link to the documentation of the respective
tool or command,
* `Snakefile`s pass the linting (`snakemake --lint`),
* `Snakefile`s are formatted with
[snakefmt](https://github.com/snakemake/snakefmt),
* Python wrapper scripts are formatted with
[black](https://black.readthedocs.io).
* Conda environments use a minimal amount of channels, in recommended
ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as
conda-forge should have highest priority and defaults channels are
usually not needed because most packages are in conda-forge nowadays).
---
 bio/samtools/fastq/separate/test/Snakefile |  2 +-
 bio/samtools/fastq/separate/wrapper.py     | 42 +++++++++-------------
 2 files changed, 18 insertions(+), 26 deletions(-)

diff --git a/bio/samtools/fastq/separate/test/Snakefile b/bio/samtools/fastq/separate/test/Snakefile
index eb899a1a953..7c8a38be419 100644
--- a/bio/samtools/fastq/separate/test/Snakefile
+++ b/bio/samtools/fastq/separate/test/Snakefile
@@ -7,7 +7,7 @@ rule samtools_fastq_separate:
     log:
         "{sample}.separate.log",
     params:
-        sort="-m 4G",
+        collate="",
         fastq="-n",
     # Remember, this is the number of samtools' additional threads. At least 2 threads have to be requested on cluster sumbission. This value - 2 will be sent to samtools sort -@ argument.
     threads: 3
diff --git a/bio/samtools/fastq/separate/wrapper.py b/bio/samtools/fastq/separate/wrapper.py
index d4f8d1b0ffd..581a192099b 100644
--- a/bio/samtools/fastq/separate/wrapper.py
+++ b/bio/samtools/fastq/separate/wrapper.py
@@ -10,37 +10,29 @@
 from snakemake.shell import shell
 from snakemake_wrapper_utils.snakemake import get_mem
 
-params_sort = snakemake.params.get("sort", "")
+params_collate = snakemake.params.get("collate", "")
 params_fastq = snakemake.params.get("fastq", "")
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
 # Samtools takes additional threads through its option -@
-# One thread is used bu Samtools sort
+# One thread is used by Samtools collate
 # One thread is used by Samtools fastq
 # So snakemake.threads has to take them into account
 # before allowing additional threads through samtools sort -@
 threads = 0 if snakemake.threads <= 2 else snakemake.threads - 2
 
-mem = get_mem(snakemake, "MiB")
-mem = "-m {0:.0f}M".format(mem / threads) if mem and threads else ""
-
-with tempfile.TemporaryDirectory() as tmpdir:
-    tmp_prefix = Path(tmpdir) / "samtools_fastq.sort"
-
-    shell(
-        "(samtools sort -n"
-        " --threads {threads}"
-        " {mem}"
-        " -T {tmp_prefix}"
-        " {params_sort}"
-        " {snakemake.input[0]} | "
-        "samtools fastq"
-        " {params_fastq}"
-        " -1 {snakemake.output[0]}"
-        " -2 {snakemake.output[1]}"
-        " -0 /dev/null"
-        " -s /dev/null"
-        " -F 0x900"
-        " - "
-        ") {log}"
-    )
+shell(
+    "(samtools collate -u -O"
+    " --threads {threads}"
+    " {params_collate}"
+    " {snakemake.input[0]} | "
+    "samtools fastq"
+    " {params_fastq}"
+    " -1 {snakemake.output[0]}"
+    " -2 {snakemake.output[1]}"
+    " -0 /dev/null"
+    " -s /dev/null"
+    " -F 0x900"
+    " - "
+    ") {log}"
+)

From 847ab1d918c09908bcdb40fa3413b6dbc88d4803 Mon Sep 17 00:00:00 2001
From: tdayris <thibault.dayris@outlook.fr>
Date: Wed, 29 May 2024 09:46:37 +0200
Subject: [PATCH 23/41] feat: All ngsderive subcommands (#2732)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

<!-- Ensure that the PR title follows conventional commit style (<type>:
<description>)-->
<!-- Possible types are here:
https://github.com/commitizen/conventional-commit-types/blob/master/index.json
-->

<!-- Add a description of your PR here-->

This PR adds all [ngsderive](https://github.com/stjudecloud/ngsderive)
subcommands in a single wrapper, just like XSV and SeqKit.

### QC
<!-- Make sure that you can tick the boxes below. -->

* [X] I confirm that:

For all wrappers added by this PR,

* there is a test case which covers any introduced changes,
* `input:` and `output:` file paths in the resulting rule can be changed
arbitrarily,
* either the wrapper can only use a single core, or the example rule
contains a `threads: x` statement with `x` being a reasonable default,
* rule names in the test case are in
[snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell
what the rule is about or match the tools purpose or name (e.g.,
`map_reads` for a step that maps reads),
* all `environment.yaml` specifications follow [the respective best
practices](https://stackoverflow.com/a/64594513/2352071),
* the `environment.yaml` pinning has been updated by running
`snakedeploy pin-conda-envs environment.yaml` on a linux machine,
* wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`),
* all fields of the example rules in the `Snakefile`s and their entries
are explained via comments (`input:`/`output:`/`params:` etc.),
* `stderr` and/or `stdout` are logged correctly (`log:`), depending on
the wrapped tool,
* temporary files are either written to a unique hidden folder in the
working directory, or (better) stored where the Python function
`tempfile.gettempdir()` points to (see
[here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir);
this also means that using any Python `tempfile` default behavior
works),
* the `meta.yaml` contains a link to the documentation of the respective
tool or command,
* `Snakefile`s pass the linting (`snakemake --lint`),
* `Snakefile`s are formatted with
[snakefmt](https://github.com/snakemake/snakefmt),
* Python wrapper scripts are formatted with
[black](https://black.readthedocs.io).
* Conda environments use a minimal amount of channels, in recommended
ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as
conda-forge should have highest priority and defaults channels are
usually not needed because most packages are in conda-forge nowadays).

---------

Co-authored-by: tdayris <tdayris@gustaveroussy.fr>
Co-authored-by: tdayris <thibault.dayris@gustaveroussy.fr>
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Co-authored-by: Felix Mölder <felix.moelder@uni-due.de>
Co-authored-by: Christopher Schröder <christopher.schroeder@tu-dortmund.de>
Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>
---
 bio/ngsderive/environment.linux-64.pin.txt    | 113 ++++++++++++++++++
 bio/ngsderive/environment.yaml                |   6 +
 bio/ngsderive/meta.yaml                       |  16 +++
 bio/ngsderive/test/A.rg.bam                   | Bin 0 -> 321 bytes
 bio/ngsderive/test/A.rg.bam.bai               | Bin 0 -> 176 bytes
 bio/ngsderive/test/Snakefile                  | 101 ++++++++++++++++
 bio/ngsderive/test/annotation.sorted.gtf.gz   | Bin 0 -> 314 bytes
 .../test/annotation.sorted.gtf.gz.tbi         | Bin 0 -> 128 bytes
 bio/ngsderive/wrapper.py                      |  40 +++++++
 test.py                                       |  39 ++++++
 10 files changed, 315 insertions(+)
 create mode 100644 bio/ngsderive/environment.linux-64.pin.txt
 create mode 100644 bio/ngsderive/environment.yaml
 create mode 100644 bio/ngsderive/meta.yaml
 create mode 100644 bio/ngsderive/test/A.rg.bam
 create mode 100644 bio/ngsderive/test/A.rg.bam.bai
 create mode 100644 bio/ngsderive/test/Snakefile
 create mode 100644 bio/ngsderive/test/annotation.sorted.gtf.gz
 create mode 100644 bio/ngsderive/test/annotation.sorted.gtf.gz.tbi
 create mode 100644 bio/ngsderive/wrapper.py

diff --git a/bio/ngsderive/environment.linux-64.pin.txt b/bio/ngsderive/environment.linux-64.pin.txt
new file mode 100644
index 00000000000..0eac4c8b52d
--- /dev/null
+++ b/bio/ngsderive/environment.linux-64.pin.txt
@@ -0,0 +1,113 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.9-4_cp39.conda#bfe4b3259a8ac6cdf0037752904da6a7
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
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+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
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+https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67
+https://conda.anaconda.org/bioconda/linux-64/pysam-0.22.0-py39hcada746_1.tar.bz2#44fe602980bf98c124db2488498c5d36
+https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.9.0-pyhd8ed1ab_0.conda#2cf4264fffb9e6eff6031c5b6884d61c
+https://conda.anaconda.org/conda-forge/linux-64/aws-c-s3-0.5.2-h4ad9680_0.conda#d50162d0e3a1c74885d8281455d8e7c2
+https://conda.anaconda.org/conda-forge/linux-64/libgoogle-cloud-storage-2.21.0-hc7a4891_2.conda#cc54c794dac0d76eb1adaf6172e9c59e
+https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.4-py39h474f0d3_0.conda#aa265f5697237aa13cc10f53fa8acc4f
+https://conda.anaconda.org/bioconda/noarch/tabix-1.11-hdfd78af_0.tar.bz2#cb68d74b5a5ca94b745ce168b1043dfd
+https://conda.anaconda.org/conda-forge/linux-64/aws-crt-cpp-0.26.2-h19f5d62_7.conda#e49b978ccc14c1a34374fac693b3a998
+https://conda.anaconda.org/conda-forge/linux-64/pandas-2.2.1-py39hddac248_0.conda#85293a042c24a08e71b7608ee66b6134
+https://conda.anaconda.org/conda-forge/linux-64/polars-0.20.14-py39h2e8484c_0.conda#d8057e5c2fd2e68f9edd7700c771f6b1
+https://conda.anaconda.org/conda-forge/linux-64/aws-sdk-cpp-1.11.267-h5606698_1.conda#2f2f24cc595d2de8365e257050845c30
+https://conda.anaconda.org/conda-forge/linux-64/libarrow-15.0.0-h5001e6d_7_cpu.conda#3249fb87b4f2c207e1ff5fbcd44ec0df
+https://conda.anaconda.org/conda-forge/linux-64/libarrow-acero-15.0.0-h59595ed_7_cpu.conda#ee028786f388781b75937af244af17c1
+https://conda.anaconda.org/conda-forge/linux-64/libarrow-flight-15.0.0-hf334d8d_7_cpu.conda#baa6de62c8c19f48dca73fe246690f8b
+https://conda.anaconda.org/conda-forge/linux-64/libarrow-gandiva-15.0.0-h3f306ff_7_cpu.conda#25d20f9bfb833f5f658f230c8ba1a161
+https://conda.anaconda.org/conda-forge/linux-64/libparquet-15.0.0-h352af49_7_cpu.conda#5a5fd8d60cfb3fc35341e88fed6c0644
+https://conda.anaconda.org/conda-forge/linux-64/libarrow-dataset-15.0.0-h59595ed_7_cpu.conda#161b5f7569be51035242bcfbfaa1b504
+https://conda.anaconda.org/conda-forge/linux-64/libarrow-flight-sql-15.0.0-h469e5c9_7_cpu.conda#9947074ba2851e03dea90df356b903e3
+https://conda.anaconda.org/conda-forge/linux-64/libarrow-substrait-15.0.0-h469e5c9_7_cpu.conda#9b49ca045cc212b4139a16c14e11491b
+https://conda.anaconda.org/conda-forge/linux-64/pyarrow-15.0.0-py39h6925388_7_cpu.conda#29d642951dd0ed8d1ee6ebd311beea1a
+https://conda.anaconda.org/bioconda/noarch/gtfparse-2.5.0-pyh7cba7a3_0.tar.bz2#ea40e62a70c5b458cba8eb9f5b92cfe0
+https://conda.anaconda.org/bioconda/noarch/ngsderive-3.3.2-pyhdfd78af_0.tar.bz2#4e92e01625deca7753de5111de4aedf3
diff --git a/bio/ngsderive/environment.yaml b/bio/ngsderive/environment.yaml
new file mode 100644
index 00000000000..595a4bafc86
--- /dev/null
+++ b/bio/ngsderive/environment.yaml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - ngsderive=3.3.2
diff --git a/bio/ngsderive/meta.yaml b/bio/ngsderive/meta.yaml
new file mode 100644
index 00000000000..e333726ec74
--- /dev/null
+++ b/bio/ngsderive/meta.yaml
@@ -0,0 +1,16 @@
+name: ngsderive
+description: Backwards computing information from next-generation sequencing data and annotating splice junctions
+url: "https://github.com/stjudecloud/ngsderive"
+authors:
+  - "Thibault Dayris"
+input:
+  - ngs: "Path to BAM/SAM/Fastq file. SAM/BAM files should be indexed."
+  - gene_model: "Path to sorted GTF/GFF file. Should be tabix indexed."
+output:
+  - tsv: Path to output file
+  - junctions: Optional path to junction directory, or list of paths to junction files with a common prefix
+params:
+  - subcommand: Name of the `ngsderive` subcommand
+  - extra: Optional parameters, besides `-o`, `-g`
+notes: |
+  GTF/GFF will be automatically sorted and tabix-indexed by `ngsderive` if needed.
diff --git a/bio/ngsderive/test/A.rg.bam b/bio/ngsderive/test/A.rg.bam
new file mode 100644
index 0000000000000000000000000000000000000000..093786060d0d5960d1d7d7e167c92aeb7fd56557
GIT binary patch
literal 321
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zyPtZSZmuoupVAqq^;7j`Uyikyv&y41=}#doB2P8NGp)|G@Ju*W(eTMoKR-0{cV+d;
zQwtn+-U<0ETg<LEcacV}@a=xLjJ>O-^~Ifee!1$IjqNqj@>_T3HRkvzzPGwowtj=4
z(Y^hG$Hi>qzwCaqWp#PWhSiLFA{jpR{n>nfNfYPco(IKe^o-sJ`m9?h;iqxJCA#y%
zv@<4Gjx}D|+jd|NkNSNUsb8_rB<tn=DOlVJe6P>c^>RPQqJDiF^|VJv85tPl(E>@D
Kff*cTAOZly0EsC8

literal 0
HcmV?d00001

diff --git a/bio/ngsderive/test/A.rg.bam.bai b/bio/ngsderive/test/A.rg.bam.bai
new file mode 100644
index 0000000000000000000000000000000000000000..44316981db202c5c2e91374e602e73f2a2ec3df3
GIT binary patch
literal 176
zcmZ>A^kigWU|;}YPay^dMj(9<h(W*^!~p`YNf3E-ai}yz5s(D&VQP@ggPFs?pbFLk
OGY?%Hn|TN|5NiN7kOwaS

literal 0
HcmV?d00001

diff --git a/bio/ngsderive/test/Snakefile b/bio/ngsderive/test/Snakefile
new file mode 100644
index 00000000000..ed09b2ab1f0
--- /dev/null
+++ b/bio/ngsderive/test/Snakefile
@@ -0,0 +1,101 @@
+rule test_ngsderive_endedness:
+    input:
+        ngs="A.rg.bam",
+    output:
+        tsv="A.endedness.tsv",
+    log:
+        "ngsderive/endedness.log",
+    params:
+        command="endedness",
+        extra="-n 2 --lenient",
+    wrapper:
+        "master/bio/ngsderive"
+
+
+rule test_ngsderive_junction_annotation:
+    input:
+        ngs="A.rg.bam",
+        gene_model="annotation.sorted.gtf.gz",
+    output:
+        tsv="A.junctions.tsv",
+        junction_dir=directory("junctions"),
+    log:
+        "ngsderive/junctions.log",
+    params:
+        command="junction-annotation",
+        extra="-i 2 -c",
+    wrapper:
+        "master/bio/ngsderive"
+
+
+rule test_ngsderive_junction_annotation_list:
+    input:
+        ngs="A.rg.bam",
+        gene_model="annotation.sorted.gtf.gz",
+    output:
+        tsv="A.junctions_list.tsv",
+        junction_dir=["junctions/A.rg.bam.junctions.tsv"],
+    log:
+        "ngsderive/junctions.log",
+    params:
+        command="junction-annotation",
+        extra="-i 2 -c",
+    wrapper:
+        "master/bio/ngsderive"        
+
+
+rule test_ngsderive_strandeness:
+    input:
+        ngs="A.rg.bam",
+        gene_model="annotation.sorted.gtf.gz",
+    output:
+        tsv="A.strandedness.tsv",
+    log:
+        "ngsderive/strand.log",
+    params:
+        command="strandedness",
+        extra="--verbose -m 2 -n 1",
+    wrapper:
+        "master/bio/ngsderive"
+
+
+rule test_ngsderive_encoding:
+    input:
+        ngs="A.rg.bam",
+    output:
+        tsv="A.encoding.tsv",
+    log:
+        "ngsderive/encoding.log",
+    params:
+        command="encoding",
+        extra="-n 2",
+    wrapper:
+        "master/bio/ngsderive"
+
+
+rule test_ngsderive_instrument:
+    input:
+        ngs="A.rg.bam",
+    output:
+        tsv="A.instrument.tsv",
+    log:
+        "ngsderive/instrument.log",
+    params:
+        command="instrument",
+        extra="-n 2 -v",
+    wrapper:
+        "master/bio/ngsderive"
+
+
+rule test_ngsderive_readlen:
+    input:
+        ngs="A.rg.bam",
+    output:
+        tsv="A.readlen.tsv",
+    log:
+        "ngsderive/readlen.log",
+    params:
+        command="readlen",
+        extra="-c 0.1 -n 2",
+    wrapper:
+        "master/bio/ngsderive"
diff --git a/bio/ngsderive/test/annotation.sorted.gtf.gz b/bio/ngsderive/test/annotation.sorted.gtf.gz
new file mode 100644
index 0000000000000000000000000000000000000000..121fec87d04468e250be1b2a205ca66f66f86d7d
GIT binary patch
literal 314
zcmb2|=3rp}f&Xj_PR>jWvW#aZpUygLAmDoaRd~nEX>8sB8Wo|=FV@X2%TGx!VC_^<
zxw)i1K0w(%>QjKsqzd)e^H<MI<x`GdB<wYTO;pG&&S;ZDe~RF>r7?jK`|9_k9%i@X
z4QjvUxmLsGxU8y~$3s)Sxp}$0B6WWs=c#V}Z|1Skv2}v|hKhaLop#>xdVKy}(uNMz
z`IjeM<gZnnfBD~y!tnn`jO|4KS@v$ZcRnI^aq$i<cG03&uFeaE{I1p8L?>_g`c%p~
zCOF}-O5y6OUyYBf4O^OJE_&<2dD(WUsJp(~=lF>)sneTQ#%wcDwXA2UQm<;An77Vf
z*$tN?w9?|L3yr5$D0z#Y`yk+5F7`@p+KrfLbqq^i@rlh~V_=X+3ms_&W^iDE2msb6
BemDRC

literal 0
HcmV?d00001

diff --git a/bio/ngsderive/test/annotation.sorted.gtf.gz.tbi b/bio/ngsderive/test/annotation.sorted.gtf.gz.tbi
new file mode 100644
index 0000000000000000000000000000000000000000..c65b9b22df38181d9ebc70fc0c08e5f2ff4dab62
GIT binary patch
literal 128
zcmb2|=3rp}f&Xj_PR>jW$qczY8+jWHcv#N+MKmyG%wTX^z+H4Q#m6U6$TD!<#*(W0
z#iD^Sj7A$6e!n*=C|KkWSsT3Z$@e-(b-Rng^~vXN6->S%{dY}z^B;y+8dmEr0F9PM
NvqPGJ8Ehqp005h6C=mbv

literal 0
HcmV?d00001

diff --git a/bio/ngsderive/wrapper.py b/bio/ngsderive/wrapper.py
new file mode 100644
index 00000000000..e6e29c9479e
--- /dev/null
+++ b/bio/ngsderive/wrapper.py
@@ -0,0 +1,40 @@
+# coding: utf-8
+
+__author__ = "Thibault Dayris"
+__mail__ = "thibault.dayris@gustaveroussy.fr"
+__copyright__ = "Copyright 2024, Thibault Dayris"
+__license__ = "MIT"
+
+from os.path import commonprefix, dirname
+from snakemake import shell
+from warnings import warn
+
+extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
+gene_model = snakemake.input.get("gene_model", "")
+if gene_model:
+    gene_model = f"--gene-model {gene_model}"
+
+
+junction_dir = snakemake.output.get("junction_dir", "")
+if isinstance(junction_dir, list):
+    junction_dir = commonprefix([dirname(fp) for fp in junction_dir])
+    if not junction_dir:
+        warn(
+            "No common prefix was found within the list of "
+            "files given as `junction_files_dir`. Falling "
+            "back to default ngsderive value"
+        )
+
+if junction_dir:
+    junction_dir = f"--junction-files-dir {junction_dir}"
+
+
+shell(
+    "ngsderive {snakemake.params.command} "
+    "{extra} {gene_model} {junction_dir} "
+    "{snakemake.input.ngs} "
+    "--outfile {snakemake.output.tsv} "
+    "{log} "
+)
diff --git a/test.py b/test.py
index df62e06ed0c..8ab245518f1 100644
--- a/test.py
+++ b/test.py
@@ -3658,6 +3658,45 @@ def test_nanosimh():
     )
 
 
+@skip_if_not_modified
+def test_ngsderive():
+    run(
+        "bio/ngsderive",
+        ["snakemake", "--cores", "1", "--use-conda", "-F", "A.readlen.tsv"],
+    )
+    run(
+        "bio/ngsderive",
+        ["snakemake", "--cores", "1", "--use-conda", "-F", "A.instrument.tsv"],
+    )
+    run(
+        "bio/ngsderive",
+        ["snakemake", "--cores", "1", "--use-conda", "-F", "A.strandedness.tsv"],
+    )
+    run(
+        "bio/ngsderive",
+        ["snakemake", "--cores", "1", "--use-conda", "-F", "A.encoding.tsv"],
+    )
+    run(
+        "bio/ngsderive",
+        ["snakemake", "--cores", "1", "--use-conda", "-F", "A.junctions.tsv"],
+    )
+    run(
+        "bio/ngsderive",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "--use-conda",
+            "-F",
+            "junctions/A.rg.bam.junctions.tsv",
+        ],
+    )
+    run(
+        "bio/ngsderive",
+        ["snakemake", "--cores", "1", "--use-conda", "-F", "A.endedness.tsv"],
+    )
+
+
 @skip_if_not_modified
 def test_ngs_disambiguate():
     run(

From 83754dd9f158ea978faa1ed33668a6dda648cdb7 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 31 May 2024 01:42:29 +0000
Subject: [PATCH 24/41] perf: autobump bio/bwa/mem-samblaster (#2961)

Automatic bump of bio/bwa/mem-samblaster.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 .../mem-samblaster/environment.linux-64.pin.txt  | 16 ++++++++--------
 bio/bwa/mem-samblaster/environment.yaml          |  2 +-
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/bio/bwa/mem-samblaster/environment.linux-64.pin.txt b/bio/bwa/mem-samblaster/environment.linux-64.pin.txt
index a09872d3864..2cc609d630f 100644
--- a/bio/bwa/mem-samblaster/environment.linux-64.pin.txt
+++ b/bio/bwa/mem-samblaster/environment.linux-64.pin.txt
@@ -3,21 +3,21 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
-https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125
 https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.4-hcb278e6_0.conda#318b08df404f9c9be5712aaa5a6f0bb0
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
-https://conda.anaconda.org/bioconda/linux-64/samblaster-0.1.26-h4ac6f70_4.tar.bz2#ec247b30a124fca1bd48a709c15739ec
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/bioconda/linux-64/samblaster-0.1.26-h4ac6f70_5.tar.bz2#a75893fa748b34123082ea21d4df229a
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
 https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda#f2cfec9406850991f4e3d960cc9e3321
-https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
+https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h4ab18f5_6.conda#559d338a4234c2ad6e676f460a093e67
 https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.18-he4a0461_0.tar.bz2#848d5a392a3a38545c42b1a079ca27c0
 https://conda.anaconda.org/conda-forge/linux-64/libllvm12-12.0.1-hf817b99_2.tar.bz2#dd23dea4ce9818bc420fe53a47e8764e
 https://conda.anaconda.org/conda-forge/linux-64/ldc-1.28.1-hcf88599_0.tar.bz2#2a72ea7786be25e98de98eb572a6ff4d
-https://conda.anaconda.org/bioconda/linux-64/sambamba-1.0-h98b6b92_0.tar.bz2#ac3123bb79fd0d4e66d1d658555b6516
+https://conda.anaconda.org/bioconda/linux-64/sambamba-1.0.1-h6f6fda4_0.tar.bz2#feeba874a4da94e5b53912b8d940d845
diff --git a/bio/bwa/mem-samblaster/environment.yaml b/bio/bwa/mem-samblaster/environment.yaml
index ec5da8a2c52..c3879aebd70 100644
--- a/bio/bwa/mem-samblaster/environment.yaml
+++ b/bio/bwa/mem-samblaster/environment.yaml
@@ -4,5 +4,5 @@ channels:
   - nodefaults
 dependencies:
   - bwa =0.7.18
-  - sambamba =1.0
+  - sambamba =1.0.1
   - samblaster =0.1.26

From ff613f37f857f23d19e4dc0cace22b02113a7e07 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 31 May 2024 01:53:34 +0000
Subject: [PATCH 25/41] perf: autobump bio/bwa-mem2/mem-samblaster (#2962)

Automatic bump of bio/bwa-mem2/mem-samblaster.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 .../environment.linux-64.pin.txt               | 18 +++++++++---------
 bio/bwa-mem2/mem-samblaster/environment.yaml   |  2 +-
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/bio/bwa-mem2/mem-samblaster/environment.linux-64.pin.txt b/bio/bwa-mem2/mem-samblaster/environment.linux-64.pin.txt
index dcd1e4e2fbf..8ddfdf094ba 100644
--- a/bio/bwa-mem2/mem-samblaster/environment.linux-64.pin.txt
+++ b/bio/bwa-mem2/mem-samblaster/environment.linux-64.pin.txt
@@ -3,19 +3,19 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda#9172c297304f2a20134fc56c97fbe229
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda#e2042154faafe61969556f28bade94b9
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff
-https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54
-https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125
 https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.4-hcb278e6_0.conda#318b08df404f9c9be5712aaa5a6f0bb0
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_1.conda#e05410383ad9c39aaa76675a7661db24
-https://conda.anaconda.org/bioconda/linux-64/samblaster-0.1.26-h4ac6f70_4.tar.bz2#ec247b30a124fca1bd48a709c15739ec
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/bioconda/linux-64/samblaster-0.1.26-h4ac6f70_5.tar.bz2#a75893fa748b34123082ea21d4df229a
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
 https://conda.anaconda.org/bioconda/linux-64/bwa-mem2-2.2.1-hd03093a_5.tar.bz2#a8de1b9c3db53f3436e06f86997b5316
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
-https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
+https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h4ab18f5_6.conda#559d338a4234c2ad6e676f460a093e67
 https://conda.anaconda.org/conda-forge/linux-64/libllvm12-12.0.1-hf817b99_2.tar.bz2#dd23dea4ce9818bc420fe53a47e8764e
 https://conda.anaconda.org/conda-forge/linux-64/ldc-1.28.1-hcf88599_0.tar.bz2#2a72ea7786be25e98de98eb572a6ff4d
-https://conda.anaconda.org/bioconda/linux-64/sambamba-1.0-h98b6b92_0.tar.bz2#ac3123bb79fd0d4e66d1d658555b6516
+https://conda.anaconda.org/bioconda/linux-64/sambamba-1.0.1-h6f6fda4_0.tar.bz2#feeba874a4da94e5b53912b8d940d845
diff --git a/bio/bwa-mem2/mem-samblaster/environment.yaml b/bio/bwa-mem2/mem-samblaster/environment.yaml
index 649b1f82582..0354bb46105 100644
--- a/bio/bwa-mem2/mem-samblaster/environment.yaml
+++ b/bio/bwa-mem2/mem-samblaster/environment.yaml
@@ -4,5 +4,5 @@ channels:
   - nodefaults
 dependencies:
   - bwa-mem2 =2.2.1
-  - sambamba =1.0
+  - sambamba =1.0.1
   - samblaster =0.1.26

From 7a0d553e09921cebc77b54d314c211b91099f7bd Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 31 May 2024 02:32:58 +0000
Subject: [PATCH 26/41] perf: autobump bio/freebayes (#2963)

Automatic bump of bio/freebayes.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 bio/freebayes/environment.linux-64.pin.txt | 30 +++++++++++-----------
 bio/freebayes/environment.yaml             |  2 +-
 2 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/bio/freebayes/environment.linux-64.pin.txt b/bio/freebayes/environment.linux-64.pin.txt
index 1efd1ded748..8ab7ef6b851 100644
--- a/bio/freebayes/environment.linux-64.pin.txt
+++ b/bio/freebayes/environment.linux-64.pin.txt
@@ -4,12 +4,12 @@
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_1.conda#33b7851c39c25da14f6a233a8ccbeeca
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
 https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
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@@ -19,34 +19,34 @@ https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda
 https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d
 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-ha4646dd_5.conda#7a6bd7a12a4bd359e2afe6c0fa1acace
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-hca663fb_7.conda#c0bd771f09a326fdcd95a60b617795bf
 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7
 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
-https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c
 https://conda.anaconda.org/conda-forge/linux-64/sed-4.8-he412f7d_0.tar.bz2#7362f0042e95681f5d371c46c83ebd08
-https://conda.anaconda.org/bioconda/linux-64/wfa2-lib-2.3.4-h4ac6f70_1.tar.bz2#d4960247cfc981ce600ef4f5c0a67ab0
+https://conda.anaconda.org/bioconda/linux-64/wfa2-lib-2.3.5-h4ac6f70_0.tar.bz2#6e462242b628a90a06fe64c8e8fac0cf
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
 https://conda.anaconda.org/bioconda/linux-64/bedtools-2.31.1-hf5e1c6e_1.tar.bz2#2066287e826a2ff469fa0b62b24b6059
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_5.conda#e73e9cfd1191783392131e6238bdb3e9
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_7.conda#1b84f26d9f4f6026e179e7805d5a15cd
 https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a
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 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
-https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
-https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
+https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h4ab18f5_6.conda#559d338a4234c2ad6e676f460a093e67
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
 https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_h413a1c8_0.conda#a356024784da6dfd4683dc5ecf45b155
-https://conda.anaconda.org/conda-forge/linux-64/parallel-20240322-ha770c72_0.conda#5ad3f5eb0086ae5ca3cf926c0773b844
+https://conda.anaconda.org/conda-forge/linux-64/parallel-20240522-ha770c72_0.conda#95444bc23d494d0b06405bea54c7cd1f
 https://conda.anaconda.org/conda-forge/linux-64/python-3.12.3-hab00c5b_0_cpython.conda#2540b74d304f71d3e89c81209db4db84
 https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-22_linux64_openblas.conda#1a2a0cd3153464fee6646f3dd6dad9b8
-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.7.1-hca28451_0.conda#755c7f876815003337d2c61ff5d047e5
-https://conda.anaconda.org/conda-forge/noarch/setuptools-69.5.1-pyhd8ed1ab_0.conda#7462280d81f639363e6e63c81276bd9e
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_0.conda#f21c27f076a07907e70c49bb57bd0f20
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda#c8ddb4f34a208df4dd42509a0f6a1c89
 https://conda.anaconda.org/bioconda/noarch/snakemake-wrapper-utils-0.6.2-pyhdfd78af_0.tar.bz2#fd8759bbd04116eace828c4fab906096
 https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae
 https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h81da01d_0.tar.bz2#1084947eefd2bbe9c1f84ca24061a9d5
diff --git a/bio/freebayes/environment.yaml b/bio/freebayes/environment.yaml
index a87d084bfe3..5313ad3820e 100644
--- a/bio/freebayes/environment.yaml
+++ b/bio/freebayes/environment.yaml
@@ -7,7 +7,7 @@ dependencies:
   - bcftools =1.20
   - vcflib =1.0.9
   - htslib =1.20
-  - parallel =20240322
+  - parallel =20240522
   - bedtools =2.31.1
   - sed =4.8
   - snakemake-wrapper-utils =0.6.2

From df82b381a49b7810087f73b7c83db4fff6d57b66 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 31 May 2024 03:23:07 +0000
Subject: [PATCH 27/41] perf: autobump bio/ngsderive (#2964)

Automatic bump of bio/ngsderive.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 bio/ngsderive/environment.linux-64.pin.txt | 122 ++++++++++-----------
 bio/ngsderive/environment.yaml             |   2 +-
 2 files changed, 57 insertions(+), 67 deletions(-)

diff --git a/bio/ngsderive/environment.linux-64.pin.txt b/bio/ngsderive/environment.linux-64.pin.txt
index 0eac4c8b52d..51f6598721e 100644
--- a/bio/ngsderive/environment.linux-64.pin.txt
+++ b/bio/ngsderive/environment.linux-64.pin.txt
@@ -4,110 +4,100 @@
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_1.conda#33b7851c39c25da14f6a233a8ccbeeca
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.9-4_cp39.conda#bfe4b3259a8ac6cdf0037752904da6a7
 https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
-https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.9.13-hd590300_0.conda#0ba89522712d993987e6d0fae108c721
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
+https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.9.19-h4ab18f5_0.conda#c6dedd5eab2236f4abb59ade9fb7fd44
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-https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.27.0-hd590300_0.conda#f6afff0e9ee08d2f1b897881a4f38cdb
+https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
 https://conda.anaconda.org/conda-forge/linux-64/gflags-2.2.2-he1b5a44_1004.tar.bz2#cddaf2c63ea4a5901cf09524c490ecdc
-https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda#cc47e1facc155f91abd89b11e48e72ff
 https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
-https://conda.anaconda.org/conda-forge/linux-64/libabseil-20240116.1-cxx17_h59595ed_2.conda#75648bc5dd3b8eab22406876c24d81ec
+https://conda.anaconda.org/conda-forge/linux-64/libabseil-20240116.2-cxx17_h59595ed_0.conda#682bdbe046a68f749769b492f3625c5c
 https://conda.anaconda.org/conda-forge/linux-64/libbrotlicommon-1.1.0-hd590300_1.conda#aec6c91c7371c26392a06708a73c70e5
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-https://conda.anaconda.org/conda-forge/linux-64/pyarrow-15.0.0-py39h6925388_7_cpu.conda#29d642951dd0ed8d1ee6ebd311beea1a
+https://conda.anaconda.org/conda-forge/linux-64/aws-crt-cpp-0.26.9-he3a8b3b_0.conda#fbe6a256dd70a505730e7c461cd37a35
+https://conda.anaconda.org/conda-forge/linux-64/pandas-2.2.2-py39hfc16268_1.conda#8b23d2b425035a7468d17e6fe1d54124
+https://conda.anaconda.org/conda-forge/linux-64/polars-0.20.30-py39ha963410_0.conda#322084e8890afc27fcca6df7a528df25
+https://conda.anaconda.org/conda-forge/linux-64/aws-sdk-cpp-1.11.329-hba8bd5f_3.conda#720494d9f06b4aff1270cffb7acc7920
+https://conda.anaconda.org/conda-forge/linux-64/libarrow-16.1.0-hcb6531f_6_cpu.conda#0df3fc2a8d63b1cc49973c5a679ec438
+https://conda.anaconda.org/conda-forge/linux-64/libarrow-acero-16.1.0-hac33072_6_cpu.conda#38b1161e2f8c72095f64ea35ee1294c5
+https://conda.anaconda.org/conda-forge/linux-64/libparquet-16.1.0-h6a7eafb_6_cpu.conda#87f676c6cb33f8e1956948ee216fa3a1
+https://conda.anaconda.org/conda-forge/linux-64/pyarrow-core-16.1.0-py39h176f5a7_1_cpu.conda#2b7f2d25781b16fcea840fee27b2f62f
+https://conda.anaconda.org/conda-forge/linux-64/libarrow-dataset-16.1.0-hac33072_6_cpu.conda#2e9430df8ffd645a5bc7edffb252c3de
+https://conda.anaconda.org/conda-forge/linux-64/libarrow-substrait-16.1.0-h7e0c224_6_cpu.conda#81fea801c4bb126509e784cbd2ca4d17
+https://conda.anaconda.org/conda-forge/linux-64/pyarrow-16.1.0-py39h8003fee_1.conda#af311215d24d386ddf77bef64bb6e9c9
 https://conda.anaconda.org/bioconda/noarch/gtfparse-2.5.0-pyh7cba7a3_0.tar.bz2#ea40e62a70c5b458cba8eb9f5b92cfe0
 https://conda.anaconda.org/bioconda/noarch/ngsderive-3.3.2-pyhdfd78af_0.tar.bz2#4e92e01625deca7753de5111de4aedf3
diff --git a/bio/ngsderive/environment.yaml b/bio/ngsderive/environment.yaml
index 595a4bafc86..11560495447 100644
--- a/bio/ngsderive/environment.yaml
+++ b/bio/ngsderive/environment.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - ngsderive=3.3.2
+  - ngsderive =3.3.2

From 9b371ca6014a38cf23e78598638e4c709a5e82af Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 31 May 2024 03:35:47 +0000
Subject: [PATCH 28/41] perf: autobump bio/open-cravat/run (#2965)

Automatic bump of bio/open-cravat/run.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 .../run/environment.linux-64.pin.txt          | 26 +++++++++----------
 bio/open-cravat/run/environment.yaml          |  2 +-
 2 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/bio/open-cravat/run/environment.linux-64.pin.txt b/bio/open-cravat/run/environment.linux-64.pin.txt
index 59c12f7d8d9..fa1435eb37d 100644
--- a/bio/open-cravat/run/environment.linux-64.pin.txt
+++ b/bio/open-cravat/run/environment.linux-64.pin.txt
@@ -4,26 +4,26 @@
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda#10569984e7db886e4f1abc2b47ad79a1
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h95c4c6d_6.conda#3cfab3e709f77e9f1b3d380eb622494a
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_1.conda#33b7851c39c25da14f6a233a8ccbeeca
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-4_cp312.conda#dccc2d142812964fcc6abdc97b672dff
 https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-hc881cc4_6.conda#aae89d3736661c36a5591788aebd0817
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-hc881cc4_6.conda#df88796bd09a0d2ed292e59101478ad8
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
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-https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-h43f5ff8_6.conda#e54a5ddc67e673f9105cf2a2e9c070b0
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-hca663fb_7.conda#c0bd771f09a326fdcd95a60b617795bf
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 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
-https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
 https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2#4cb3ad778ec2d5a7acbdf254eb1c42ae
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_6.conda#3666a850342f8f3be88f9a93d948d027
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_7.conda#1b84f26d9f4f6026e179e7805d5a15cd
 https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.3-h2797004_0.conda#b3316cbe90249da4f8e84cd66e1cc55b
 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
@@ -46,7 +46,7 @@ https://conda.anaconda.org/bioconda/noarch/pyliftover-0.4-py_0.tar.bz2#9b2bbe0d1
 https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha2e5f31_6.tar.bz2#2a7de29fb590ca14b5243c4c812c8025
 https://conda.anaconda.org/bioconda/noarch/pyvcf3-1.0.3-pyhdfd78af_0.tar.bz2#2471bf4fad9f15602ad24164adf1a22a
 https://conda.anaconda.org/conda-forge/linux-64/pyyaml-6.0.1-py312h98912ed_1.conda#e3fd78d8d490af1d84763b9fe3f2e552
-https://conda.anaconda.org/conda-forge/noarch/setuptools-69.5.1-pyhd8ed1ab_0.conda#7462280d81f639363e6e63c81276bd9e
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda#c8ddb4f34a208df4dd42509a0f6a1c89
 https://conda.anaconda.org/conda-forge/noarch/sortedcontainers-2.4.0-pyhd8ed1ab_0.tar.bz2#6d6552722448103793743dabfbda532d
 https://conda.anaconda.org/bioconda/noarch/twobitreader-3.1.7-pyh864c0ab_1.tar.bz2#5ec5a0c9b2b017d0fa99060d6b97639d
 https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.11.0-pyha770c72_0.conda#6ef2fc37559256cf682d8b3375e89b80
@@ -66,10 +66,10 @@ https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.11.0-hd8ed1ab_
 https://conda.anaconda.org/conda-forge/noarch/urllib3-2.2.1-pyhd8ed1ab_0.conda#08807a87fa7af10754d46f63b368e016
 https://conda.anaconda.org/conda-forge/linux-64/yarl-1.9.4-py312h98912ed_0.conda#ec3eb4803df33e90a41bc216a68d02f1
 https://conda.anaconda.org/conda-forge/linux-64/aiohttp-3.9.5-py312h98912ed_0.conda#edc01db954d139fe398a5f378f96ab4d
-https://conda.anaconda.org/conda-forge/noarch/aiosqlite-0.19.0-pyhd8ed1ab_0.conda#c60a47f9f29057417165a8af579396a8
+https://conda.anaconda.org/conda-forge/noarch/aiosqlite-0.20.0-pyhd8ed1ab_0.conda#4904ac8e78fa697150e874e4b2dbf6e5
 https://conda.anaconda.org/conda-forge/noarch/markdown-3.6-pyhd8ed1ab_0.conda#06e9bebf748a0dea03ecbe1f0e27e909
 https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.4-py312heda63a1_0.conda#d8285bea2a350f63fab23bf460221f3f
-https://conda.anaconda.org/conda-forge/noarch/requests-2.31.0-pyhd8ed1ab_0.conda#a30144e4156cdbb236f99ebb49828f8b
+https://conda.anaconda.org/conda-forge/noarch/requests-2.32.3-pyhd8ed1ab_0.conda#5ede4753180c7a550a443c430dc8ab52
 https://conda.anaconda.org/conda-forge/linux-64/biopython-1.83-py312h98912ed_0.conda#53e12da7730d109fddca08aef28a4a50
 https://conda.anaconda.org/conda-forge/noarch/requests-toolbelt-1.0.0-pyhd8ed1ab_0.conda#99c98318c8646b08cc764f90ce98906e
-https://conda.anaconda.org/bioconda/noarch/open-cravat-2.6.0-pyhdfd78af_0.tar.bz2#3fe73bfc0028b28184021c0d5b1472ec
+https://conda.anaconda.org/bioconda/noarch/open-cravat-2.6.1-pyhdfd78af_0.tar.bz2#b53e50da0f8796571eef7c39fbfd3545
diff --git a/bio/open-cravat/run/environment.yaml b/bio/open-cravat/run/environment.yaml
index 6370c49eb27..8c7c987c6b9 100644
--- a/bio/open-cravat/run/environment.yaml
+++ b/bio/open-cravat/run/environment.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - open-cravat =2.6.0
+  - open-cravat =2.6.1

From f1ffa3eee366cba828314cc9a368ba69f17d98c2 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 31 May 2024 03:45:11 +0000
Subject: [PATCH 29/41] perf: autobump bio/open-cravat/module (#2966)

Automatic bump of bio/open-cravat/module.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 .../module/environment.linux-64.pin.txt       | 26 +++++++++----------
 bio/open-cravat/module/environment.yaml       |  2 +-
 2 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/bio/open-cravat/module/environment.linux-64.pin.txt b/bio/open-cravat/module/environment.linux-64.pin.txt
index 59c12f7d8d9..fa1435eb37d 100644
--- a/bio/open-cravat/module/environment.linux-64.pin.txt
+++ b/bio/open-cravat/module/environment.linux-64.pin.txt
@@ -4,26 +4,26 @@
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda#10569984e7db886e4f1abc2b47ad79a1
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h95c4c6d_6.conda#3cfab3e709f77e9f1b3d380eb622494a
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_1.conda#33b7851c39c25da14f6a233a8ccbeeca
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-4_cp312.conda#dccc2d142812964fcc6abdc97b672dff
 https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-hc881cc4_6.conda#aae89d3736661c36a5591788aebd0817
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-hc881cc4_6.conda#df88796bd09a0d2ed292e59101478ad8
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
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-https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-h43f5ff8_6.conda#e54a5ddc67e673f9105cf2a2e9c070b0
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-hca663fb_7.conda#c0bd771f09a326fdcd95a60b617795bf
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 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
-https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
 https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2#4cb3ad778ec2d5a7acbdf254eb1c42ae
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_6.conda#3666a850342f8f3be88f9a93d948d027
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_7.conda#1b84f26d9f4f6026e179e7805d5a15cd
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@@ -46,7 +46,7 @@ https://conda.anaconda.org/bioconda/noarch/pyliftover-0.4-py_0.tar.bz2#9b2bbe0d1
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 https://conda.anaconda.org/conda-forge/linux-64/pyyaml-6.0.1-py312h98912ed_1.conda#e3fd78d8d490af1d84763b9fe3f2e552
-https://conda.anaconda.org/conda-forge/noarch/setuptools-69.5.1-pyhd8ed1ab_0.conda#7462280d81f639363e6e63c81276bd9e
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda#c8ddb4f34a208df4dd42509a0f6a1c89
 https://conda.anaconda.org/conda-forge/noarch/sortedcontainers-2.4.0-pyhd8ed1ab_0.tar.bz2#6d6552722448103793743dabfbda532d
 https://conda.anaconda.org/bioconda/noarch/twobitreader-3.1.7-pyh864c0ab_1.tar.bz2#5ec5a0c9b2b017d0fa99060d6b97639d
 https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.11.0-pyha770c72_0.conda#6ef2fc37559256cf682d8b3375e89b80
@@ -66,10 +66,10 @@ https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.11.0-hd8ed1ab_
 https://conda.anaconda.org/conda-forge/noarch/urllib3-2.2.1-pyhd8ed1ab_0.conda#08807a87fa7af10754d46f63b368e016
 https://conda.anaconda.org/conda-forge/linux-64/yarl-1.9.4-py312h98912ed_0.conda#ec3eb4803df33e90a41bc216a68d02f1
 https://conda.anaconda.org/conda-forge/linux-64/aiohttp-3.9.5-py312h98912ed_0.conda#edc01db954d139fe398a5f378f96ab4d
-https://conda.anaconda.org/conda-forge/noarch/aiosqlite-0.19.0-pyhd8ed1ab_0.conda#c60a47f9f29057417165a8af579396a8
+https://conda.anaconda.org/conda-forge/noarch/aiosqlite-0.20.0-pyhd8ed1ab_0.conda#4904ac8e78fa697150e874e4b2dbf6e5
 https://conda.anaconda.org/conda-forge/noarch/markdown-3.6-pyhd8ed1ab_0.conda#06e9bebf748a0dea03ecbe1f0e27e909
 https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.4-py312heda63a1_0.conda#d8285bea2a350f63fab23bf460221f3f
-https://conda.anaconda.org/conda-forge/noarch/requests-2.31.0-pyhd8ed1ab_0.conda#a30144e4156cdbb236f99ebb49828f8b
+https://conda.anaconda.org/conda-forge/noarch/requests-2.32.3-pyhd8ed1ab_0.conda#5ede4753180c7a550a443c430dc8ab52
 https://conda.anaconda.org/conda-forge/linux-64/biopython-1.83-py312h98912ed_0.conda#53e12da7730d109fddca08aef28a4a50
 https://conda.anaconda.org/conda-forge/noarch/requests-toolbelt-1.0.0-pyhd8ed1ab_0.conda#99c98318c8646b08cc764f90ce98906e
-https://conda.anaconda.org/bioconda/noarch/open-cravat-2.6.0-pyhdfd78af_0.tar.bz2#3fe73bfc0028b28184021c0d5b1472ec
+https://conda.anaconda.org/bioconda/noarch/open-cravat-2.6.1-pyhdfd78af_0.tar.bz2#b53e50da0f8796571eef7c39fbfd3545
diff --git a/bio/open-cravat/module/environment.yaml b/bio/open-cravat/module/environment.yaml
index 6370c49eb27..8c7c987c6b9 100644
--- a/bio/open-cravat/module/environment.yaml
+++ b/bio/open-cravat/module/environment.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - open-cravat =2.6.0
+  - open-cravat =2.6.1

From 191542d475853f6f19495e136e105970928a9fd8 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 31 May 2024 04:30:04 +0000
Subject: [PATCH 30/41] perf: autobump bio/sambamba/markdup (#2968)

Automatic bump of bio/sambamba/markdup.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 .../markdup/environment.linux-64.pin.txt         | 16 ++++++++--------
 bio/sambamba/markdup/environment.yaml            |  2 +-
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/bio/sambamba/markdup/environment.linux-64.pin.txt b/bio/sambamba/markdup/environment.linux-64.pin.txt
index 9f76fe263f6..261f900619a 100644
--- a/bio/sambamba/markdup/environment.linux-64.pin.txt
+++ b/bio/sambamba/markdup/environment.linux-64.pin.txt
@@ -3,17 +3,17 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda#9172c297304f2a20134fc56c97fbe229
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda#e2042154faafe61969556f28bade94b9
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff
-https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54
-https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125
 https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.4-hcb278e6_0.conda#318b08df404f9c9be5712aaa5a6f0bb0
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_2.conda#7dbaa197d7ba6032caf7ae7f32c1efa0
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
-https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
+https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h4ab18f5_6.conda#559d338a4234c2ad6e676f460a093e67
 https://conda.anaconda.org/conda-forge/linux-64/libllvm12-12.0.1-hf817b99_2.tar.bz2#dd23dea4ce9818bc420fe53a47e8764e
 https://conda.anaconda.org/conda-forge/linux-64/ldc-1.28.1-hcf88599_0.tar.bz2#2a72ea7786be25e98de98eb572a6ff4d
-https://conda.anaconda.org/bioconda/linux-64/sambamba-1.0-h98b6b92_0.tar.bz2#ac3123bb79fd0d4e66d1d658555b6516
+https://conda.anaconda.org/bioconda/linux-64/sambamba-1.0.1-h6f6fda4_0.tar.bz2#feeba874a4da94e5b53912b8d940d845
diff --git a/bio/sambamba/markdup/environment.yaml b/bio/sambamba/markdup/environment.yaml
index f7e0821d7f4..73bf574d495 100644
--- a/bio/sambamba/markdup/environment.yaml
+++ b/bio/sambamba/markdup/environment.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - sambamba =1.0
+  - sambamba =1.0.1

From e25b8409af3cc9e591b5106f1ebb00289f628207 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 31 May 2024 04:34:07 +0000
Subject: [PATCH 31/41] perf: autobump bio/seqkit (#2969)

Automatic bump of bio/seqkit.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 bio/seqkit/environment.linux-64.pin.txt | 2 +-
 bio/seqkit/environment.yaml             | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/bio/seqkit/environment.linux-64.pin.txt b/bio/seqkit/environment.linux-64.pin.txt
index b0bbfaff99f..ef7f2286175 100644
--- a/bio/seqkit/environment.linux-64.pin.txt
+++ b/bio/seqkit/environment.linux-64.pin.txt
@@ -2,4 +2,4 @@
 # $ conda create --name <env> --file <this file>
 # platform: linux-64
 @EXPLICIT
-https://conda.anaconda.org/bioconda/linux-64/seqkit-2.8.1-h9ee0642_0.tar.bz2#ad5ff56e35cfd6ba3e53c7f711457fcf
+https://conda.anaconda.org/bioconda/linux-64/seqkit-2.8.2-h9ee0642_0.tar.bz2#f929883f8d0304106efdfeced55698c7
diff --git a/bio/seqkit/environment.yaml b/bio/seqkit/environment.yaml
index 4da25522ea5..fd59801b3c8 100644
--- a/bio/seqkit/environment.yaml
+++ b/bio/seqkit/environment.yaml
@@ -2,4 +2,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - seqkit =2.8.1
+  - seqkit =2.8.2

From 613e55d915215348651e878fe37f6533e6d77363 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 31 May 2024 04:38:10 +0000
Subject: [PATCH 32/41] perf: autobump bio/sambamba/view (#2970)

Automatic bump of bio/sambamba/view.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 bio/sambamba/view/environment.linux-64.pin.txt | 16 ++++++++--------
 bio/sambamba/view/environment.yaml             |  2 +-
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/bio/sambamba/view/environment.linux-64.pin.txt b/bio/sambamba/view/environment.linux-64.pin.txt
index 9f76fe263f6..261f900619a 100644
--- a/bio/sambamba/view/environment.linux-64.pin.txt
+++ b/bio/sambamba/view/environment.linux-64.pin.txt
@@ -3,17 +3,17 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda#9172c297304f2a20134fc56c97fbe229
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda#e2042154faafe61969556f28bade94b9
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff
-https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54
-https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125
 https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.4-hcb278e6_0.conda#318b08df404f9c9be5712aaa5a6f0bb0
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_2.conda#7dbaa197d7ba6032caf7ae7f32c1efa0
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
-https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
+https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h4ab18f5_6.conda#559d338a4234c2ad6e676f460a093e67
 https://conda.anaconda.org/conda-forge/linux-64/libllvm12-12.0.1-hf817b99_2.tar.bz2#dd23dea4ce9818bc420fe53a47e8764e
 https://conda.anaconda.org/conda-forge/linux-64/ldc-1.28.1-hcf88599_0.tar.bz2#2a72ea7786be25e98de98eb572a6ff4d
-https://conda.anaconda.org/bioconda/linux-64/sambamba-1.0-h98b6b92_0.tar.bz2#ac3123bb79fd0d4e66d1d658555b6516
+https://conda.anaconda.org/bioconda/linux-64/sambamba-1.0.1-h6f6fda4_0.tar.bz2#feeba874a4da94e5b53912b8d940d845
diff --git a/bio/sambamba/view/environment.yaml b/bio/sambamba/view/environment.yaml
index f7e0821d7f4..73bf574d495 100644
--- a/bio/sambamba/view/environment.yaml
+++ b/bio/sambamba/view/environment.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - sambamba =1.0
+  - sambamba =1.0.1

From 88ac3f6dfae93606f74ae8c88b6f8b9e2d059a02 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 31 May 2024 04:39:46 +0000
Subject: [PATCH 33/41] perf: autobump bio/sambamba/slice (#2972)

Automatic bump of bio/sambamba/slice.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 bio/sambamba/slice/environment.linux-64.pin.txt | 16 ++++++++--------
 bio/sambamba/slice/environment.yaml             |  2 +-
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/bio/sambamba/slice/environment.linux-64.pin.txt b/bio/sambamba/slice/environment.linux-64.pin.txt
index 9f76fe263f6..261f900619a 100644
--- a/bio/sambamba/slice/environment.linux-64.pin.txt
+++ b/bio/sambamba/slice/environment.linux-64.pin.txt
@@ -3,17 +3,17 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda#9172c297304f2a20134fc56c97fbe229
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda#e2042154faafe61969556f28bade94b9
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff
-https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54
-https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125
 https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.4-hcb278e6_0.conda#318b08df404f9c9be5712aaa5a6f0bb0
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_2.conda#7dbaa197d7ba6032caf7ae7f32c1efa0
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
-https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
+https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h4ab18f5_6.conda#559d338a4234c2ad6e676f460a093e67
 https://conda.anaconda.org/conda-forge/linux-64/libllvm12-12.0.1-hf817b99_2.tar.bz2#dd23dea4ce9818bc420fe53a47e8764e
 https://conda.anaconda.org/conda-forge/linux-64/ldc-1.28.1-hcf88599_0.tar.bz2#2a72ea7786be25e98de98eb572a6ff4d
-https://conda.anaconda.org/bioconda/linux-64/sambamba-1.0-h98b6b92_0.tar.bz2#ac3123bb79fd0d4e66d1d658555b6516
+https://conda.anaconda.org/bioconda/linux-64/sambamba-1.0.1-h6f6fda4_0.tar.bz2#feeba874a4da94e5b53912b8d940d845
diff --git a/bio/sambamba/slice/environment.yaml b/bio/sambamba/slice/environment.yaml
index f7e0821d7f4..73bf574d495 100644
--- a/bio/sambamba/slice/environment.yaml
+++ b/bio/sambamba/slice/environment.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - sambamba =1.0
+  - sambamba =1.0.1

From 18359ac437bb9f1065c703b3bf2da1d3da9548be Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 31 May 2024 04:40:35 +0000
Subject: [PATCH 34/41] perf: autobump bio/sambamba/index (#2971)

Automatic bump of bio/sambamba/index.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 bio/sambamba/index/environment.linux-64.pin.txt | 16 ++++++++--------
 bio/sambamba/index/environment.yaml             |  2 +-
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/bio/sambamba/index/environment.linux-64.pin.txt b/bio/sambamba/index/environment.linux-64.pin.txt
index 9f76fe263f6..261f900619a 100644
--- a/bio/sambamba/index/environment.linux-64.pin.txt
+++ b/bio/sambamba/index/environment.linux-64.pin.txt
@@ -3,17 +3,17 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda#9172c297304f2a20134fc56c97fbe229
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda#e2042154faafe61969556f28bade94b9
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff
-https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54
-https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125
 https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.4-hcb278e6_0.conda#318b08df404f9c9be5712aaa5a6f0bb0
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_2.conda#7dbaa197d7ba6032caf7ae7f32c1efa0
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
-https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
+https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h4ab18f5_6.conda#559d338a4234c2ad6e676f460a093e67
 https://conda.anaconda.org/conda-forge/linux-64/libllvm12-12.0.1-hf817b99_2.tar.bz2#dd23dea4ce9818bc420fe53a47e8764e
 https://conda.anaconda.org/conda-forge/linux-64/ldc-1.28.1-hcf88599_0.tar.bz2#2a72ea7786be25e98de98eb572a6ff4d
-https://conda.anaconda.org/bioconda/linux-64/sambamba-1.0-h98b6b92_0.tar.bz2#ac3123bb79fd0d4e66d1d658555b6516
+https://conda.anaconda.org/bioconda/linux-64/sambamba-1.0.1-h6f6fda4_0.tar.bz2#feeba874a4da94e5b53912b8d940d845
diff --git a/bio/sambamba/index/environment.yaml b/bio/sambamba/index/environment.yaml
index f7e0821d7f4..73bf574d495 100644
--- a/bio/sambamba/index/environment.yaml
+++ b/bio/sambamba/index/environment.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - sambamba =1.0
+  - sambamba =1.0.1

From 4575792deb144dd80401d46bc2fb72175976305a Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 31 May 2024 04:46:29 +0000
Subject: [PATCH 35/41] perf: autobump bio/sambamba/flagstat (#2973)

Automatic bump of bio/sambamba/flagstat.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 .../flagstat/environment.linux-64.pin.txt        | 16 ++++++++--------
 bio/sambamba/flagstat/environment.yaml           |  2 +-
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/bio/sambamba/flagstat/environment.linux-64.pin.txt b/bio/sambamba/flagstat/environment.linux-64.pin.txt
index 9f76fe263f6..261f900619a 100644
--- a/bio/sambamba/flagstat/environment.linux-64.pin.txt
+++ b/bio/sambamba/flagstat/environment.linux-64.pin.txt
@@ -3,17 +3,17 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda#9172c297304f2a20134fc56c97fbe229
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda#e2042154faafe61969556f28bade94b9
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff
-https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54
-https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125
 https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.4-hcb278e6_0.conda#318b08df404f9c9be5712aaa5a6f0bb0
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_2.conda#7dbaa197d7ba6032caf7ae7f32c1efa0
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
-https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
+https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h4ab18f5_6.conda#559d338a4234c2ad6e676f460a093e67
 https://conda.anaconda.org/conda-forge/linux-64/libllvm12-12.0.1-hf817b99_2.tar.bz2#dd23dea4ce9818bc420fe53a47e8764e
 https://conda.anaconda.org/conda-forge/linux-64/ldc-1.28.1-hcf88599_0.tar.bz2#2a72ea7786be25e98de98eb572a6ff4d
-https://conda.anaconda.org/bioconda/linux-64/sambamba-1.0-h98b6b92_0.tar.bz2#ac3123bb79fd0d4e66d1d658555b6516
+https://conda.anaconda.org/bioconda/linux-64/sambamba-1.0.1-h6f6fda4_0.tar.bz2#feeba874a4da94e5b53912b8d940d845
diff --git a/bio/sambamba/flagstat/environment.yaml b/bio/sambamba/flagstat/environment.yaml
index f7e0821d7f4..73bf574d495 100644
--- a/bio/sambamba/flagstat/environment.yaml
+++ b/bio/sambamba/flagstat/environment.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - sambamba =1.0
+  - sambamba =1.0.1

From adf9a28b64f87aec3fa8286f356f44b6bb77561e Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 31 May 2024 04:49:22 +0000
Subject: [PATCH 36/41] perf: autobump bio/sambamba/merge (#2975)

Automatic bump of bio/sambamba/merge.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 bio/sambamba/merge/environment.linux-64.pin.txt | 16 ++++++++--------
 bio/sambamba/merge/environment.yaml             |  2 +-
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/bio/sambamba/merge/environment.linux-64.pin.txt b/bio/sambamba/merge/environment.linux-64.pin.txt
index 9f76fe263f6..261f900619a 100644
--- a/bio/sambamba/merge/environment.linux-64.pin.txt
+++ b/bio/sambamba/merge/environment.linux-64.pin.txt
@@ -3,17 +3,17 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda#9172c297304f2a20134fc56c97fbe229
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda#e2042154faafe61969556f28bade94b9
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff
-https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54
-https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125
 https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.4-hcb278e6_0.conda#318b08df404f9c9be5712aaa5a6f0bb0
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_2.conda#7dbaa197d7ba6032caf7ae7f32c1efa0
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
-https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
+https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h4ab18f5_6.conda#559d338a4234c2ad6e676f460a093e67
 https://conda.anaconda.org/conda-forge/linux-64/libllvm12-12.0.1-hf817b99_2.tar.bz2#dd23dea4ce9818bc420fe53a47e8764e
 https://conda.anaconda.org/conda-forge/linux-64/ldc-1.28.1-hcf88599_0.tar.bz2#2a72ea7786be25e98de98eb572a6ff4d
-https://conda.anaconda.org/bioconda/linux-64/sambamba-1.0-h98b6b92_0.tar.bz2#ac3123bb79fd0d4e66d1d658555b6516
+https://conda.anaconda.org/bioconda/linux-64/sambamba-1.0.1-h6f6fda4_0.tar.bz2#feeba874a4da94e5b53912b8d940d845
diff --git a/bio/sambamba/merge/environment.yaml b/bio/sambamba/merge/environment.yaml
index f7e0821d7f4..73bf574d495 100644
--- a/bio/sambamba/merge/environment.yaml
+++ b/bio/sambamba/merge/environment.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - sambamba =1.0
+  - sambamba =1.0.1

From 990e8416b730267a65ba5a97b71537655bbfe6db Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 31 May 2024 04:54:19 +0000
Subject: [PATCH 37/41] perf: autobump bio/sambamba/sort (#2976)

Automatic bump of bio/sambamba/sort.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 bio/sambamba/sort/environment.linux-64.pin.txt | 16 ++++++++--------
 bio/sambamba/sort/environment.yaml             |  2 +-
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/bio/sambamba/sort/environment.linux-64.pin.txt b/bio/sambamba/sort/environment.linux-64.pin.txt
index 9f76fe263f6..261f900619a 100644
--- a/bio/sambamba/sort/environment.linux-64.pin.txt
+++ b/bio/sambamba/sort/environment.linux-64.pin.txt
@@ -3,17 +3,17 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda#9172c297304f2a20134fc56c97fbe229
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda#e2042154faafe61969556f28bade94b9
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff
-https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54
-https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125
 https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.4-hcb278e6_0.conda#318b08df404f9c9be5712aaa5a6f0bb0
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_2.conda#7dbaa197d7ba6032caf7ae7f32c1efa0
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
-https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
+https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h4ab18f5_6.conda#559d338a4234c2ad6e676f460a093e67
 https://conda.anaconda.org/conda-forge/linux-64/libllvm12-12.0.1-hf817b99_2.tar.bz2#dd23dea4ce9818bc420fe53a47e8764e
 https://conda.anaconda.org/conda-forge/linux-64/ldc-1.28.1-hcf88599_0.tar.bz2#2a72ea7786be25e98de98eb572a6ff4d
-https://conda.anaconda.org/bioconda/linux-64/sambamba-1.0-h98b6b92_0.tar.bz2#ac3123bb79fd0d4e66d1d658555b6516
+https://conda.anaconda.org/bioconda/linux-64/sambamba-1.0.1-h6f6fda4_0.tar.bz2#feeba874a4da94e5b53912b8d940d845
diff --git a/bio/sambamba/sort/environment.yaml b/bio/sambamba/sort/environment.yaml
index f7e0821d7f4..73bf574d495 100644
--- a/bio/sambamba/sort/environment.yaml
+++ b/bio/sambamba/sort/environment.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - sambamba =1.0
+  - sambamba =1.0.1

From d8b4b5fab114c66bf712ee271b00f831a5ed558d Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 31 May 2024 05:49:40 +0000
Subject: [PATCH 38/41] perf: autobump bio/sra-tools/fasterq-dump (#2974)

Automatic bump of bio/sra-tools/fasterq-dump.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
---
 .../fasterq-dump/environment.linux-64.pin.txt | 38 +++++++++----------
 bio/sra-tools/fasterq-dump/environment.yaml   |  2 +-
 2 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/bio/sra-tools/fasterq-dump/environment.linux-64.pin.txt b/bio/sra-tools/fasterq-dump/environment.linux-64.pin.txt
index b1c357211e0..2d5ff03cbe4 100644
--- a/bio/sra-tools/fasterq-dump/environment.linux-64.pin.txt
+++ b/bio/sra-tools/fasterq-dump/environment.linux-64.pin.txt
@@ -4,31 +4,32 @@
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_1.conda#33b7851c39c25da14f6a233a8ccbeeca
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
 https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
-https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.27.0-hd590300_0.conda#f6afff0e9ee08d2f1b897881a4f38cdb
+https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
 https://conda.anaconda.org/conda-forge/linux-64/icu-70.1-h27087fc_0.tar.bz2#87473a15119779e021c314249d4b4aed
 https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
 https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
-https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.1-h59595ed_0.conda#476fb82aba5358a08d52ec44e286ce33
+https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d
 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
 https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-hd590300_2.conda#d66573916ffcf376178462f1b61c941e
 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7
 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
-https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_2.conda#7dbaa197d7ba6032caf7ae7f32c1efa0
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_0.conda#51a753e64a3027bd7e23a189b1f6e91e
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125
+https://conda.anaconda.org/bioconda/linux-64/ncbi-vdb-3.1.1-h4ac6f70_0.tar.bz2#4cbc542ee7db0710bdf07a4e55f5daaf
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-h4ab18f5_3.conda#12ea6d0d4ed54530eaed18e4835c1f7c
 https://conda.anaconda.org/conda-forge/linux-64/ossuuid-1.6.2-hf484d3e_1000.tar.bz2#0ca24876ead80a9290d3936aea5fefb1
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
 https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a
-https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.1-h2797004_0.conda#fc4ccadfbf6d4784de88c41704792562
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.3-h2797004_0.conda#b3316cbe90249da4f8e84cd66e1cc55b
 https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
 https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.9.14-h22db469_4.tar.bz2#aced7c1f4b4dbfea08e033c6ae97c53e
 https://conda.anaconda.org/conda-forge/linux-64/pbzip2-1.1.13-h1fcc475_2.conda#e1bf3c0868789f3ddf5d1aeb47bc60a6
@@ -36,8 +37,8 @@ https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.con
 https://conda.anaconda.org/conda-forge/linux-64/pigz-2.8-h2797004_0.conda#1832561770273ca7cf52b989dd83e6c3
 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
-https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
-https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
+https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h4ab18f5_6.conda#559d338a4234c2ad6e676f460a093e67
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
 https://conda.anaconda.org/conda-forge/linux-64/perl-capture-tiny-0.48-pl5321ha770c72_1.tar.bz2#4859b3d284090166394875e68184dc9c
 https://conda.anaconda.org/conda-forge/noarch/perl-constant-1.33-pl5321hd8ed1ab_0.tar.bz2#7f9fc9cfa08a3fe36ffcff820c65c3ac
@@ -52,16 +53,16 @@ https://conda.anaconda.org/conda-forge/noarch/perl-scope-guard-0.21-pl5321hd8ed1
 https://conda.anaconda.org/conda-forge/linux-64/perl-test-warnings-0.031-pl5321ha770c72_0.conda#db0eb51272ea7af7213afaaf7e9967c3
 https://conda.anaconda.org/conda-forge/linux-64/perl-try-tiny-0.31-pl5321ha770c72_0.tar.bz2#cc23b14ed56bf51d84832d98ebd156af
 https://conda.anaconda.org/conda-forge/noarch/perl-xml-sax-base-1.09-pl5321hd8ed1ab_0.tar.bz2#a4d9b02cd61c478c9cb58064307a1414
-https://conda.anaconda.org/conda-forge/linux-64/python-3.12.2-hab00c5b_0_cpython.conda#ad7b68400f3a6ebe72b00be093c7f301
-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.5.0-hca28451_0.conda#7144d5a828e2cae218e0e3c98d8a0aeb
+https://conda.anaconda.org/conda-forge/linux-64/python-3.12.3-hab00c5b_0_cpython.conda#2540b74d304f71d3e89c81209db4db84
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_0.conda#f21c27f076a07907e70c49bb57bd0f20
 https://conda.anaconda.org/conda-forge/noarch/perl-carp-1.50-pl5321hd8ed1ab_0.tar.bz2#bdddc03e28019b902da71b722f2288d7
 https://conda.anaconda.org/conda-forge/noarch/perl-file-path-2.18-pl5321hd8ed1ab_0.tar.bz2#e13e456f61b8261ba074c0aa93086afe
 https://conda.anaconda.org/conda-forge/linux-64/perl-test-fatal-0.016-pl5321ha770c72_0.tar.bz2#5c397b1fd3095004f4ff149af1c0dd3c
 https://conda.anaconda.org/conda-forge/noarch/perl-xml-namespacesupport-1.12-pl5321hd8ed1ab_0.tar.bz2#f4ce684ba66b3228bfffb09892235930
-https://conda.anaconda.org/conda-forge/noarch/setuptools-69.1.1-pyhd8ed1ab_0.conda#576de899521b7d43674ba3ef6eae9142
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda#c8ddb4f34a208df4dd42509a0f6a1c89
 https://conda.anaconda.org/bioconda/noarch/snakemake-wrapper-utils-0.6.2-pyhdfd78af_0.tar.bz2#fd8759bbd04116eace828c4fab906096
-https://conda.anaconda.org/conda-forge/noarch/wheel-0.42.0-pyhd8ed1ab_0.conda#1cdea58981c5cbc17b51973bcaddcea7
-https://conda.anaconda.org/conda-forge/linux-64/curl-8.5.0-hca28451_0.conda#e5e83fb15e752dbc8f54c4ac7da7d0f1
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae
+https://conda.anaconda.org/conda-forge/linux-64/curl-8.8.0-he654da7_0.conda#042341d8b9ba4ee7f2722b81fae9f0ad
 https://conda.anaconda.org/conda-forge/noarch/perl-business-isbn-data-20210112.006-pl5321hd8ed1ab_0.tar.bz2#a70f08650ec3919ee5e599834f1349d3
 https://conda.anaconda.org/conda-forge/noarch/perl-file-temp-0.2304-pl5321hd8ed1ab_0.tar.bz2#0a039c4fc36748942287ee10d0431515
 https://conda.anaconda.org/conda-forge/linux-64/perl-pathtools-3.75-pl5321h166bdaf_0.tar.bz2#4e72abd06ec15cb28c14798dab2c10c8
@@ -76,5 +77,4 @@ https://conda.anaconda.org/bioconda/linux-64/perl-alien-build-2.48-pl5321hec16e2
 https://conda.anaconda.org/conda-forge/linux-64/perl-uri-5.17-pl5321ha770c72_0.conda#847c007d5f4a59b356a9cd577010b89c
 https://conda.anaconda.org/bioconda/linux-64/perl-alien-libxml2-0.17-pl5321hec16e2b_0.tar.bz2#4628ba7447031d6e4661732a2e7bdc64
 https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxml-2.0207-pl5321h661654b_0.tar.bz2#1ce8ba66c656dbe547110201b1456797
-https://conda.anaconda.org/bioconda/linux-64/ncbi-vdb-3.1.0-hdbdd923_0.tar.bz2#42f40b3acb8616b7a5efee7afba13e05
-https://conda.anaconda.org/bioconda/linux-64/sra-tools-3.1.0-h9f5acd7_0.tar.bz2#dafa071fc413d51f3037064bc624342e
+https://conda.anaconda.org/bioconda/linux-64/sra-tools-3.1.1-h4304569_0.tar.bz2#0abefb12a2345d4c74c0516800f8dbc2
diff --git a/bio/sra-tools/fasterq-dump/environment.yaml b/bio/sra-tools/fasterq-dump/environment.yaml
index 1f560f9d195..ab01e94b4ce 100644
--- a/bio/sra-tools/fasterq-dump/environment.yaml
+++ b/bio/sra-tools/fasterq-dump/environment.yaml
@@ -3,7 +3,7 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - sra-tools =3.1.0
+  - sra-tools =3.1.1
   - pigz =2.8
   - pbzip2 =1.1.13
   - snakemake-wrapper-utils =0.6.2

From 9f2564323429bea84dfb0b01a5b9f53b37fa397c Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 31 May 2024 06:52:59 +0000
Subject: [PATCH 39/41] perf: autobump bio/rasusa (#2967)

Automatic bump of bio/rasusa.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>
---
 bio/rasusa/environment.linux-64.pin.txt |  6 +++---
 bio/rasusa/environment.yaml             |  2 +-
 bio/rasusa/meta.yaml                    |  4 ++--
 bio/rasusa/wrapper.py                   | 14 ++++++++------
 4 files changed, 14 insertions(+), 12 deletions(-)

diff --git a/bio/rasusa/environment.linux-64.pin.txt b/bio/rasusa/environment.linux-64.pin.txt
index 2e5cf4b5d97..1480bce84d7 100644
--- a/bio/rasusa/environment.linux-64.pin.txt
+++ b/bio/rasusa/environment.linux-64.pin.txt
@@ -3,7 +3,7 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_3.conda#7124cbb46b13d395bdde68f2d215c989
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_3.conda#23fdf1fef05baeb7eadc2aed5fb0011f
-https://conda.anaconda.org/bioconda/linux-64/rasusa-0.8.0-h031d066_0.tar.bz2#0e86b97fdc0c8ea60b8e5b7b5725eb04
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
+https://conda.anaconda.org/bioconda/linux-64/rasusa-2.0.0-h031d066_0.tar.bz2#59ca5054e6ec09ee5e7ec23c8b010a14
diff --git a/bio/rasusa/environment.yaml b/bio/rasusa/environment.yaml
index 85cc9d99764..b7847cec468 100644
--- a/bio/rasusa/environment.yaml
+++ b/bio/rasusa/environment.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - rasusa =0.8.0
+  - rasusa =2.0.0
diff --git a/bio/rasusa/meta.yaml b/bio/rasusa/meta.yaml
index fd710ef64d5..4085559f4e3 100644
--- a/bio/rasusa/meta.yaml
+++ b/bio/rasusa/meta.yaml
@@ -19,5 +19,5 @@ params:
     Alternatively, a FASTA/Q index file can be provided and the genome size will be set
     to the sum of all reference sequences. |nl|
     If ``bases`` is not provided, this option and ``coverage`` are required
-  options: >
-    Any other options as listed in `the docs <https://github.com/mbhall88/rasusa#usage>`_.
+  extra: >
+    Additional program arguments.
diff --git a/bio/rasusa/wrapper.py b/bio/rasusa/wrapper.py
index a7e88deb741..901dd3a83db 100644
--- a/bio/rasusa/wrapper.py
+++ b/bio/rasusa/wrapper.py
@@ -6,12 +6,12 @@
 
 from snakemake.shell import shell
 
-
-options = snakemake.params.get("options", "")
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+extra = snakemake.params.get("extra", "")
 
 bases = snakemake.params.get("bases")
-if bases is not None:
-    options += " -b {}".format(bases)
+if bases:
+    extra += f" --bases {bases}"
 else:
     covg = snakemake.params.get("coverage")
     gsize = snakemake.params.get("genome_size")
@@ -19,6 +19,8 @@
         raise ValueError(
             "If `bases` is not given, then `coverage` and `genome_size` must be"
         )
-    options += " -g {gsize} -c {covg}".format(gsize=gsize, covg=covg)
+    extra += f" --genome-size {gsize} --coverage {covg}"
 
-shell("rasusa {options} -i {snakemake.input} -o {snakemake.output} 2> {snakemake.log}")
+shell(
+    "rasusa reads {extra} --output {snakemake.output[0]} --output {snakemake.output[1]} {snakemake.input} {log}"
+)

From a66d1110e1793462a883ad5edd2debbac285eaa8 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Mon, 3 Jun 2024 15:50:23 +0200
Subject: [PATCH 40/41] chore: release 3.11.0 (#2925)

:robot: I have created a release \*beep\* \*boop\*
---
##
[3.11.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.10.2...v3.11.0)
(2024-05-31)


### Features

* add samtools markdup wrapper
([#2926](https://www.github.com/snakemake/snakemake-wrappers/issues/2926))
([3c86bae](https://www.github.com/snakemake/snakemake-wrappers/commit/3c86baef4586b596c6c3375336828257e8bb815f))
* Add support for regions file and arbitrary FAI/GZI paths
([#2936](https://www.github.com/snakemake/snakemake-wrappers/issues/2936))
([445b35f](https://www.github.com/snakemake/snakemake-wrappers/commit/445b35f314f035d8248ca84cb16b273b0e65847c))
* add wrapper to samtools collate
([#2929](https://www.github.com/snakemake/snakemake-wrappers/issues/2929))
([0c7ae27](https://www.github.com/snakemake/snakemake-wrappers/commit/0c7ae27622e45167b9cc1aaf1be238b0d25429b9))
* All ngsderive subcommands
([#2732](https://www.github.com/snakemake/snakemake-wrappers/issues/2732))
([847ab1d](https://www.github.com/snakemake/snakemake-wrappers/commit/847ab1d918c09908bcdb40fa3413b6dbc88d4803))
* auto infer run mode
([#2937](https://www.github.com/snakemake/snakemake-wrappers/issues/2937))
([08bd3cd](https://www.github.com/snakemake/snakemake-wrappers/commit/08bd3cd79243c4c0636f88d229667e58595611bd))
* Goleft indexcov
([#2734](https://www.github.com/snakemake/snakemake-wrappers/issues/2734))
([ebef6f8](https://www.github.com/snakemake/snakemake-wrappers/commit/ebef6f8259e89d9a06b2264a5d0a34da23d2e84e))


### Bug Fixes

* bamcoverage without effective genome size
([#2941](https://www.github.com/snakemake/snakemake-wrappers/issues/2941))
([b6ad55f](https://www.github.com/snakemake/snakemake-wrappers/commit/b6ad55f4d2c702ecc904d6b40b4b35b2463c895a))
* issue
[#366](https://www.github.com/snakemake/snakemake-wrappers/issues/366)
and
[#2649](https://www.github.com/snakemake/snakemake-wrappers/issues/2649)
([#2928](https://www.github.com/snakemake/snakemake-wrappers/issues/2928))
([e10ab57](https://www.github.com/snakemake/snakemake-wrappers/commit/e10ab571a63b36ce1295e50b6f6b7e4742e0beae))
* remove NA string replacement, fixed upstream
([#2940](https://www.github.com/snakemake/snakemake-wrappers/issues/2940))
([8f4d223](https://www.github.com/snakemake/snakemake-wrappers/commit/8f4d223ec6c1e1e2715708d0532399ede4ed2727))


### Performance Improvements

* autobump bio/bismark/bam2nuc
([#2943](https://www.github.com/snakemake/snakemake-wrappers/issues/2943))
([9228479](https://www.github.com/snakemake/snakemake-wrappers/commit/9228479896c2410ae6a58849bf59e5f01bc5e712))
* autobump bio/bismark/bismark
([#2948](https://www.github.com/snakemake/snakemake-wrappers/issues/2948))
([d9abb20](https://www.github.com/snakemake/snakemake-wrappers/commit/d9abb20e0e002d9ec16507d86211b0555a2546ba))
* autobump bio/bismark/bismark_genome_preparation
([#2945](https://www.github.com/snakemake/snakemake-wrappers/issues/2945))
([899ae0d](https://www.github.com/snakemake/snakemake-wrappers/commit/899ae0d96d04fa56a7ba5989d9dea18be0d3ebc6))
* autobump bio/bismark/bismark_methylation_extractor
([#2944](https://www.github.com/snakemake/snakemake-wrappers/issues/2944))
([1b232d2](https://www.github.com/snakemake/snakemake-wrappers/commit/1b232d24816a40f75568bec224eff4e164b3f953))
* autobump bio/bismark/bismark2bedGraph
([#2947](https://www.github.com/snakemake/snakemake-wrappers/issues/2947))
([ab29098](https://www.github.com/snakemake/snakemake-wrappers/commit/ab29098757c3eef17884f198234ec456e19414f9))
* autobump bio/bismark/bismark2report
([#2951](https://www.github.com/snakemake/snakemake-wrappers/issues/2951))
([13dd155](https://www.github.com/snakemake/snakemake-wrappers/commit/13dd155a20025b8aaaa80ce3747e6822562bb6b1))
* autobump bio/bismark/bismark2summary
([#2946](https://www.github.com/snakemake/snakemake-wrappers/issues/2946))
([bfb3d30](https://www.github.com/snakemake/snakemake-wrappers/commit/bfb3d305daa519faee4ad4ea7dbd313941f4c128))
* autobump bio/bismark/deduplicate_bismark
([#2950](https://www.github.com/snakemake/snakemake-wrappers/issues/2950))
([bcf3c06](https://www.github.com/snakemake/snakemake-wrappers/commit/bcf3c06887443dae9749254f0e8d34e30f880b7e))
* autobump bio/bowtie2/align
([#2949](https://www.github.com/snakemake/snakemake-wrappers/issues/2949))
([6b0593f](https://www.github.com/snakemake/snakemake-wrappers/commit/6b0593facfcae0b9c92cb1f31423426752c0230d))
* autobump bio/bowtie2/build
([#2942](https://www.github.com/snakemake/snakemake-wrappers/issues/2942))
([5b3ca20](https://www.github.com/snakemake/snakemake-wrappers/commit/5b3ca20635bd0e427a548e68cd8a40fdb0047f10))
* autobump bio/bwa-mem2/mem-samblaster
([#2962](https://www.github.com/snakemake/snakemake-wrappers/issues/2962))
([ff613f3](https://www.github.com/snakemake/snakemake-wrappers/commit/ff613f37f857f23d19e4dc0cace22b02113a7e07))
* autobump bio/bwa/mem-samblaster
([#2961](https://www.github.com/snakemake/snakemake-wrappers/issues/2961))
([83754dd](https://www.github.com/snakemake/snakemake-wrappers/commit/83754dd9f158ea978faa1ed33668a6dda648cdb7))
* autobump bio/fastq_screen
([#2952](https://www.github.com/snakemake/snakemake-wrappers/issues/2952))
([e45fcac](https://www.github.com/snakemake/snakemake-wrappers/commit/e45fcac221ef45f345a516bff905a53c864e7355))
* autobump bio/freebayes
([#2963](https://www.github.com/snakemake/snakemake-wrappers/issues/2963))
([7a0d553](https://www.github.com/snakemake/snakemake-wrappers/commit/7a0d553e09921cebc77b54d314c211b91099f7bd))
* autobump bio/gatk/applybqsr
([#2938](https://www.github.com/snakemake/snakemake-wrappers/issues/2938))
([498c67f](https://www.github.com/snakemake/snakemake-wrappers/commit/498c67fb12691b0021a7b234dfc279957b46708c))
* autobump bio/gatk3/realignertargetcreator
([#2931](https://www.github.com/snakemake/snakemake-wrappers/issues/2931))
([2d2835c](https://www.github.com/snakemake/snakemake-wrappers/commit/2d2835c51f974f7f45420f832b8084520d2d3ec0))
* autobump bio/gdc-api/bam-slicing
([#2954](https://www.github.com/snakemake/snakemake-wrappers/issues/2954))
([32d25c1](https://www.github.com/snakemake/snakemake-wrappers/commit/32d25c1560b4c581694c49dc6d3a596e5ca581ab))
* autobump bio/goleft/indexcov
([#2930](https://www.github.com/snakemake/snakemake-wrappers/issues/2930))
([5ccbdb0](https://www.github.com/snakemake/snakemake-wrappers/commit/5ccbdb078a835ad0c2fd3e9e63677103fe216eeb))
* autobump bio/gseapy/gsea
([#2953](https://www.github.com/snakemake/snakemake-wrappers/issues/2953))
([dda3d16](https://www.github.com/snakemake/snakemake-wrappers/commit/dda3d16c9b49145bd58d287db1021c41d5a24710))
* autobump bio/hifiasm
([#2932](https://www.github.com/snakemake/snakemake-wrappers/issues/2932))
([3722de7](https://www.github.com/snakemake/snakemake-wrappers/commit/3722de7000d0b74a3c56bfdb27aad6cf318562ee))
* autobump bio/multiqc
([#2955](https://www.github.com/snakemake/snakemake-wrappers/issues/2955))
([91ad107](https://www.github.com/snakemake/snakemake-wrappers/commit/91ad1079fa03b07f8ebb9ebf21fe92d21c8a3c13))
* autobump bio/ngsderive
([#2964](https://www.github.com/snakemake/snakemake-wrappers/issues/2964))
([df82b38](https://www.github.com/snakemake/snakemake-wrappers/commit/df82b381a49b7810087f73b7c83db4fff6d57b66))
* autobump bio/open-cravat/module
([#2966](https://www.github.com/snakemake/snakemake-wrappers/issues/2966))
([f1ffa3e](https://www.github.com/snakemake/snakemake-wrappers/commit/f1ffa3eee366cba828314cc9a368ba69f17d98c2))
* autobump bio/open-cravat/run
([#2965](https://www.github.com/snakemake/snakemake-wrappers/issues/2965))
([9b371ca](https://www.github.com/snakemake/snakemake-wrappers/commit/9b371ca6014a38cf23e78598638e4c709a5e82af))
* autobump bio/ptrimmer
([#2933](https://www.github.com/snakemake/snakemake-wrappers/issues/2933))
([cd37e0b](https://www.github.com/snakemake/snakemake-wrappers/commit/cd37e0bb19e341ad40560828f3c052ef69529088))
* autobump bio/rasusa
([#2967](https://www.github.com/snakemake/snakemake-wrappers/issues/2967))
([9f25643](https://www.github.com/snakemake/snakemake-wrappers/commit/9f2564323429bea84dfb0b01a5b9f53b37fa397c))
* autobump bio/rbt/csvreport
([#2956](https://www.github.com/snakemake/snakemake-wrappers/issues/2956))
([b2a469d](https://www.github.com/snakemake/snakemake-wrappers/commit/b2a469dc907c8f3761399affd29ca53f012cc3ee))
* autobump bio/sambamba/flagstat
([#2973](https://www.github.com/snakemake/snakemake-wrappers/issues/2973))
([4575792](https://www.github.com/snakemake/snakemake-wrappers/commit/4575792deb144dd80401d46bc2fb72175976305a))
* autobump bio/sambamba/index
([#2971](https://www.github.com/snakemake/snakemake-wrappers/issues/2971))
([18359ac](https://www.github.com/snakemake/snakemake-wrappers/commit/18359ac437bb9f1065c703b3bf2da1d3da9548be))
* autobump bio/sambamba/markdup
([#2968](https://www.github.com/snakemake/snakemake-wrappers/issues/2968))
([191542d](https://www.github.com/snakemake/snakemake-wrappers/commit/191542d475853f6f19495e136e105970928a9fd8))
* autobump bio/sambamba/merge
([#2975](https://www.github.com/snakemake/snakemake-wrappers/issues/2975))
([adf9a28](https://www.github.com/snakemake/snakemake-wrappers/commit/adf9a28b64f87aec3fa8286f356f44b6bb77561e))
* autobump bio/sambamba/slice
([#2972](https://www.github.com/snakemake/snakemake-wrappers/issues/2972))
([88ac3f6](https://www.github.com/snakemake/snakemake-wrappers/commit/88ac3f6dfae93606f74ae8c88b6f8b9e2d059a02))
* autobump bio/sambamba/sort
([#2976](https://www.github.com/snakemake/snakemake-wrappers/issues/2976))
([990e841](https://www.github.com/snakemake/snakemake-wrappers/commit/990e8416b730267a65ba5a97b71537655bbfe6db))
* autobump bio/sambamba/view
([#2970](https://www.github.com/snakemake/snakemake-wrappers/issues/2970))
([613e55d](https://www.github.com/snakemake/snakemake-wrappers/commit/613e55d915215348651e878fe37f6533e6d77363))
* autobump bio/seqkit
([#2969](https://www.github.com/snakemake/snakemake-wrappers/issues/2969))
([e25b840](https://www.github.com/snakemake/snakemake-wrappers/commit/e25b8409af3cc9e591b5106f1ebb00289f628207))
* autobump bio/sra-tools/fasterq-dump
([#2974](https://www.github.com/snakemake/snakemake-wrappers/issues/2974))
([d8b4b5f](https://www.github.com/snakemake/snakemake-wrappers/commit/d8b4b5fab114c66bf712ee271b00f831a5ed558d))
* autobump bio/unicycler
([#2957](https://www.github.com/snakemake/snakemake-wrappers/issues/2957))
([185ce7e](https://www.github.com/snakemake/snakemake-wrappers/commit/185ce7e4bd6adbdf840effa665f62e358865c8b8))
* autobump bio/vep/annotate
([#2958](https://www.github.com/snakemake/snakemake-wrappers/issues/2958))
([728658d](https://www.github.com/snakemake/snakemake-wrappers/commit/728658d5fae40ea784f7b8d3c567c4f7240ef7c7))
* autobump bio/vep/cache
([#2959](https://www.github.com/snakemake/snakemake-wrappers/issues/2959))
([f4e5b66](https://www.github.com/snakemake/snakemake-wrappers/commit/f4e5b66f8765d09d51d4a640d2d775d781c3018f))
* autobump bio/whatshap/haplotag
([#2934](https://www.github.com/snakemake/snakemake-wrappers/issues/2934))
([f0b638a](https://www.github.com/snakemake/snakemake-wrappers/commit/f0b638a55280c0727ccef5aab24e03b3d565f290))
* Update Datavzrd to 2.36.12
([#2924](https://www.github.com/snakemake/snakemake-wrappers/issues/2924))
([beb9d22](https://www.github.com/snakemake/snakemake-wrappers/commit/beb9d2231c5d59ba74f23f56bbfc5e004aa72331))
* Use samtools collate in fastq separate wrapper
([#2960](https://www.github.com/snakemake/snakemake-wrappers/issues/2960))
([9c8cf81](https://www.github.com/snakemake/snakemake-wrappers/commit/9c8cf81c1894fc019ffbf0f906eb88e0960c3e7d))
---


This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 CHANGELOG.md | 65 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 65 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2cad57292a6..48209290e81 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,70 @@
 # Changelog
 
+## [3.11.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.10.2...v3.11.0) (2024-05-31)
+
+
+### Features
+
+* add samtools markdup wrapper ([#2926](https://www.github.com/snakemake/snakemake-wrappers/issues/2926)) ([3c86bae](https://www.github.com/snakemake/snakemake-wrappers/commit/3c86baef4586b596c6c3375336828257e8bb815f))
+* Add support for regions file and arbitrary FAI/GZI paths ([#2936](https://www.github.com/snakemake/snakemake-wrappers/issues/2936)) ([445b35f](https://www.github.com/snakemake/snakemake-wrappers/commit/445b35f314f035d8248ca84cb16b273b0e65847c))
+* add wrapper to samtools collate ([#2929](https://www.github.com/snakemake/snakemake-wrappers/issues/2929)) ([0c7ae27](https://www.github.com/snakemake/snakemake-wrappers/commit/0c7ae27622e45167b9cc1aaf1be238b0d25429b9))
+* All ngsderive subcommands ([#2732](https://www.github.com/snakemake/snakemake-wrappers/issues/2732)) ([847ab1d](https://www.github.com/snakemake/snakemake-wrappers/commit/847ab1d918c09908bcdb40fa3413b6dbc88d4803))
+* auto infer run mode ([#2937](https://www.github.com/snakemake/snakemake-wrappers/issues/2937)) ([08bd3cd](https://www.github.com/snakemake/snakemake-wrappers/commit/08bd3cd79243c4c0636f88d229667e58595611bd))
+* Goleft indexcov ([#2734](https://www.github.com/snakemake/snakemake-wrappers/issues/2734)) ([ebef6f8](https://www.github.com/snakemake/snakemake-wrappers/commit/ebef6f8259e89d9a06b2264a5d0a34da23d2e84e))
+
+
+### Bug Fixes
+
+* bamcoverage without effective genome size ([#2941](https://www.github.com/snakemake/snakemake-wrappers/issues/2941)) ([b6ad55f](https://www.github.com/snakemake/snakemake-wrappers/commit/b6ad55f4d2c702ecc904d6b40b4b35b2463c895a))
+* issue [#366](https://www.github.com/snakemake/snakemake-wrappers/issues/366) and [#2649](https://www.github.com/snakemake/snakemake-wrappers/issues/2649) ([#2928](https://www.github.com/snakemake/snakemake-wrappers/issues/2928)) ([e10ab57](https://www.github.com/snakemake/snakemake-wrappers/commit/e10ab571a63b36ce1295e50b6f6b7e4742e0beae))
+* remove NA string replacement, fixed upstream ([#2940](https://www.github.com/snakemake/snakemake-wrappers/issues/2940)) ([8f4d223](https://www.github.com/snakemake/snakemake-wrappers/commit/8f4d223ec6c1e1e2715708d0532399ede4ed2727))
+
+
+### Performance Improvements
+
+* autobump bio/bismark/bam2nuc ([#2943](https://www.github.com/snakemake/snakemake-wrappers/issues/2943)) ([9228479](https://www.github.com/snakemake/snakemake-wrappers/commit/9228479896c2410ae6a58849bf59e5f01bc5e712))
+* autobump bio/bismark/bismark ([#2948](https://www.github.com/snakemake/snakemake-wrappers/issues/2948)) ([d9abb20](https://www.github.com/snakemake/snakemake-wrappers/commit/d9abb20e0e002d9ec16507d86211b0555a2546ba))
+* autobump bio/bismark/bismark_genome_preparation ([#2945](https://www.github.com/snakemake/snakemake-wrappers/issues/2945)) ([899ae0d](https://www.github.com/snakemake/snakemake-wrappers/commit/899ae0d96d04fa56a7ba5989d9dea18be0d3ebc6))
+* autobump bio/bismark/bismark_methylation_extractor ([#2944](https://www.github.com/snakemake/snakemake-wrappers/issues/2944)) ([1b232d2](https://www.github.com/snakemake/snakemake-wrappers/commit/1b232d24816a40f75568bec224eff4e164b3f953))
+* autobump bio/bismark/bismark2bedGraph ([#2947](https://www.github.com/snakemake/snakemake-wrappers/issues/2947)) ([ab29098](https://www.github.com/snakemake/snakemake-wrappers/commit/ab29098757c3eef17884f198234ec456e19414f9))
+* autobump bio/bismark/bismark2report ([#2951](https://www.github.com/snakemake/snakemake-wrappers/issues/2951)) ([13dd155](https://www.github.com/snakemake/snakemake-wrappers/commit/13dd155a20025b8aaaa80ce3747e6822562bb6b1))
+* autobump bio/bismark/bismark2summary ([#2946](https://www.github.com/snakemake/snakemake-wrappers/issues/2946)) ([bfb3d30](https://www.github.com/snakemake/snakemake-wrappers/commit/bfb3d305daa519faee4ad4ea7dbd313941f4c128))
+* autobump bio/bismark/deduplicate_bismark ([#2950](https://www.github.com/snakemake/snakemake-wrappers/issues/2950)) ([bcf3c06](https://www.github.com/snakemake/snakemake-wrappers/commit/bcf3c06887443dae9749254f0e8d34e30f880b7e))
+* autobump bio/bowtie2/align ([#2949](https://www.github.com/snakemake/snakemake-wrappers/issues/2949)) ([6b0593f](https://www.github.com/snakemake/snakemake-wrappers/commit/6b0593facfcae0b9c92cb1f31423426752c0230d))
+* autobump bio/bowtie2/build ([#2942](https://www.github.com/snakemake/snakemake-wrappers/issues/2942)) ([5b3ca20](https://www.github.com/snakemake/snakemake-wrappers/commit/5b3ca20635bd0e427a548e68cd8a40fdb0047f10))
+* autobump bio/bwa-mem2/mem-samblaster ([#2962](https://www.github.com/snakemake/snakemake-wrappers/issues/2962)) ([ff613f3](https://www.github.com/snakemake/snakemake-wrappers/commit/ff613f37f857f23d19e4dc0cace22b02113a7e07))
+* autobump bio/bwa/mem-samblaster ([#2961](https://www.github.com/snakemake/snakemake-wrappers/issues/2961)) ([83754dd](https://www.github.com/snakemake/snakemake-wrappers/commit/83754dd9f158ea978faa1ed33668a6dda648cdb7))
+* autobump bio/fastq_screen ([#2952](https://www.github.com/snakemake/snakemake-wrappers/issues/2952)) ([e45fcac](https://www.github.com/snakemake/snakemake-wrappers/commit/e45fcac221ef45f345a516bff905a53c864e7355))
+* autobump bio/freebayes ([#2963](https://www.github.com/snakemake/snakemake-wrappers/issues/2963)) ([7a0d553](https://www.github.com/snakemake/snakemake-wrappers/commit/7a0d553e09921cebc77b54d314c211b91099f7bd))
+* autobump bio/gatk/applybqsr ([#2938](https://www.github.com/snakemake/snakemake-wrappers/issues/2938)) ([498c67f](https://www.github.com/snakemake/snakemake-wrappers/commit/498c67fb12691b0021a7b234dfc279957b46708c))
+* autobump bio/gatk3/realignertargetcreator ([#2931](https://www.github.com/snakemake/snakemake-wrappers/issues/2931)) ([2d2835c](https://www.github.com/snakemake/snakemake-wrappers/commit/2d2835c51f974f7f45420f832b8084520d2d3ec0))
+* autobump bio/gdc-api/bam-slicing ([#2954](https://www.github.com/snakemake/snakemake-wrappers/issues/2954)) ([32d25c1](https://www.github.com/snakemake/snakemake-wrappers/commit/32d25c1560b4c581694c49dc6d3a596e5ca581ab))
+* autobump bio/goleft/indexcov ([#2930](https://www.github.com/snakemake/snakemake-wrappers/issues/2930)) ([5ccbdb0](https://www.github.com/snakemake/snakemake-wrappers/commit/5ccbdb078a835ad0c2fd3e9e63677103fe216eeb))
+* autobump bio/gseapy/gsea ([#2953](https://www.github.com/snakemake/snakemake-wrappers/issues/2953)) ([dda3d16](https://www.github.com/snakemake/snakemake-wrappers/commit/dda3d16c9b49145bd58d287db1021c41d5a24710))
+* autobump bio/hifiasm ([#2932](https://www.github.com/snakemake/snakemake-wrappers/issues/2932)) ([3722de7](https://www.github.com/snakemake/snakemake-wrappers/commit/3722de7000d0b74a3c56bfdb27aad6cf318562ee))
+* autobump bio/multiqc ([#2955](https://www.github.com/snakemake/snakemake-wrappers/issues/2955)) ([91ad107](https://www.github.com/snakemake/snakemake-wrappers/commit/91ad1079fa03b07f8ebb9ebf21fe92d21c8a3c13))
+* autobump bio/ngsderive ([#2964](https://www.github.com/snakemake/snakemake-wrappers/issues/2964)) ([df82b38](https://www.github.com/snakemake/snakemake-wrappers/commit/df82b381a49b7810087f73b7c83db4fff6d57b66))
+* autobump bio/open-cravat/module ([#2966](https://www.github.com/snakemake/snakemake-wrappers/issues/2966)) ([f1ffa3e](https://www.github.com/snakemake/snakemake-wrappers/commit/f1ffa3eee366cba828314cc9a368ba69f17d98c2))
+* autobump bio/open-cravat/run ([#2965](https://www.github.com/snakemake/snakemake-wrappers/issues/2965)) ([9b371ca](https://www.github.com/snakemake/snakemake-wrappers/commit/9b371ca6014a38cf23e78598638e4c709a5e82af))
+* autobump bio/ptrimmer ([#2933](https://www.github.com/snakemake/snakemake-wrappers/issues/2933)) ([cd37e0b](https://www.github.com/snakemake/snakemake-wrappers/commit/cd37e0bb19e341ad40560828f3c052ef69529088))
+* autobump bio/rasusa ([#2967](https://www.github.com/snakemake/snakemake-wrappers/issues/2967)) ([9f25643](https://www.github.com/snakemake/snakemake-wrappers/commit/9f2564323429bea84dfb0b01a5b9f53b37fa397c))
+* autobump bio/rbt/csvreport ([#2956](https://www.github.com/snakemake/snakemake-wrappers/issues/2956)) ([b2a469d](https://www.github.com/snakemake/snakemake-wrappers/commit/b2a469dc907c8f3761399affd29ca53f012cc3ee))
+* autobump bio/sambamba/flagstat ([#2973](https://www.github.com/snakemake/snakemake-wrappers/issues/2973)) ([4575792](https://www.github.com/snakemake/snakemake-wrappers/commit/4575792deb144dd80401d46bc2fb72175976305a))
+* autobump bio/sambamba/index ([#2971](https://www.github.com/snakemake/snakemake-wrappers/issues/2971)) ([18359ac](https://www.github.com/snakemake/snakemake-wrappers/commit/18359ac437bb9f1065c703b3bf2da1d3da9548be))
+* autobump bio/sambamba/markdup ([#2968](https://www.github.com/snakemake/snakemake-wrappers/issues/2968)) ([191542d](https://www.github.com/snakemake/snakemake-wrappers/commit/191542d475853f6f19495e136e105970928a9fd8))
+* autobump bio/sambamba/merge ([#2975](https://www.github.com/snakemake/snakemake-wrappers/issues/2975)) ([adf9a28](https://www.github.com/snakemake/snakemake-wrappers/commit/adf9a28b64f87aec3fa8286f356f44b6bb77561e))
+* autobump bio/sambamba/slice ([#2972](https://www.github.com/snakemake/snakemake-wrappers/issues/2972)) ([88ac3f6](https://www.github.com/snakemake/snakemake-wrappers/commit/88ac3f6dfae93606f74ae8c88b6f8b9e2d059a02))
+* autobump bio/sambamba/sort ([#2976](https://www.github.com/snakemake/snakemake-wrappers/issues/2976)) ([990e841](https://www.github.com/snakemake/snakemake-wrappers/commit/990e8416b730267a65ba5a97b71537655bbfe6db))
+* autobump bio/sambamba/view ([#2970](https://www.github.com/snakemake/snakemake-wrappers/issues/2970)) ([613e55d](https://www.github.com/snakemake/snakemake-wrappers/commit/613e55d915215348651e878fe37f6533e6d77363))
+* autobump bio/seqkit ([#2969](https://www.github.com/snakemake/snakemake-wrappers/issues/2969)) ([e25b840](https://www.github.com/snakemake/snakemake-wrappers/commit/e25b8409af3cc9e591b5106f1ebb00289f628207))
+* autobump bio/sra-tools/fasterq-dump ([#2974](https://www.github.com/snakemake/snakemake-wrappers/issues/2974)) ([d8b4b5f](https://www.github.com/snakemake/snakemake-wrappers/commit/d8b4b5fab114c66bf712ee271b00f831a5ed558d))
+* autobump bio/unicycler ([#2957](https://www.github.com/snakemake/snakemake-wrappers/issues/2957)) ([185ce7e](https://www.github.com/snakemake/snakemake-wrappers/commit/185ce7e4bd6adbdf840effa665f62e358865c8b8))
+* autobump bio/vep/annotate ([#2958](https://www.github.com/snakemake/snakemake-wrappers/issues/2958)) ([728658d](https://www.github.com/snakemake/snakemake-wrappers/commit/728658d5fae40ea784f7b8d3c567c4f7240ef7c7))
+* autobump bio/vep/cache ([#2959](https://www.github.com/snakemake/snakemake-wrappers/issues/2959)) ([f4e5b66](https://www.github.com/snakemake/snakemake-wrappers/commit/f4e5b66f8765d09d51d4a640d2d775d781c3018f))
+* autobump bio/whatshap/haplotag ([#2934](https://www.github.com/snakemake/snakemake-wrappers/issues/2934)) ([f0b638a](https://www.github.com/snakemake/snakemake-wrappers/commit/f0b638a55280c0727ccef5aab24e03b3d565f290))
+* Update Datavzrd to 2.36.12 ([#2924](https://www.github.com/snakemake/snakemake-wrappers/issues/2924)) ([beb9d22](https://www.github.com/snakemake/snakemake-wrappers/commit/beb9d2231c5d59ba74f23f56bbfc5e004aa72331))
+* Use samtools collate in fastq separate wrapper ([#2960](https://www.github.com/snakemake/snakemake-wrappers/issues/2960)) ([9c8cf81](https://www.github.com/snakemake/snakemake-wrappers/commit/9c8cf81c1894fc019ffbf0f906eb88e0960c3e7d))
+
 ### [3.10.2](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.10.1...v3.10.2) (2024-05-03)
 
 

From 1e9e511fdf14174c52ae7555fb78e416986503be Mon Sep 17 00:00:00 2001
From: "Filipe G. Vieira" <1151762+fgvieira@users.noreply.github.com>
Date: Tue, 4 Jun 2024 20:25:16 +0200
Subject: [PATCH 41/41] feat: Support lists in param.region, and fix typo
 (#2978)

<!-- Ensure that the PR title follows conventional commit style (<type>:
<description>)-->
<!-- Possible types are here:
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### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] I confirm that:

For all wrappers added by this PR,

* there is a test case which covers any introduced changes,
* `input:` and `output:` file paths in the resulting rule can be changed
arbitrarily,
* either the wrapper can only use a single core, or the example rule
contains a `threads: x` statement with `x` being a reasonable default,
* rule names in the test case are in
[snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell
what the rule is about or match the tools purpose or name (e.g.,
`map_reads` for a step that maps reads),
* all `environment.yaml` specifications follow [the respective best
practices](https://stackoverflow.com/a/64594513/2352071),
* the `environment.yaml` pinning has been updated by running
`snakedeploy pin-conda-envs environment.yaml` on a linux machine,
* wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`),
* all fields of the example rules in the `Snakefile`s and their entries
are explained via comments (`input:`/`output:`/`params:` etc.),
* `stderr` and/or `stdout` are logged correctly (`log:`), depending on
the wrapped tool,
* temporary files are either written to a unique hidden folder in the
working directory, or (better) stored where the Python function
`tempfile.gettempdir()` points to (see
[here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir);
this also means that using any Python `tempfile` default behavior
works),
* the `meta.yaml` contains a link to the documentation of the respective
tool or command,
* `Snakefile`s pass the linting (`snakemake --lint`),
* `Snakefile`s are formatted with
[snakefmt](https://github.com/snakemake/snakefmt),
* Python wrapper scripts are formatted with
[black](https://black.readthedocs.io).
* Conda environments use a minimal amount of channels, in recommended
ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as
conda-forge should have highest priority and defaults channels are
usually not needed because most packages are in conda-forge nowadays).
---
 bio/samtools/faidx/test/Snakefile      | 27 ++++++++++++++++++++------
 bio/samtools/faidx/test/genome.regions |  1 +
 bio/samtools/faidx/wrapper.py          |  3 ++-
 test.py                                |  5 +++--
 4 files changed, 27 insertions(+), 9 deletions(-)
 create mode 100644 bio/samtools/faidx/test/genome.regions

diff --git a/bio/samtools/faidx/test/Snakefile b/bio/samtools/faidx/test/Snakefile
index d15d6fba505..cf366a4235c 100644
--- a/bio/samtools/faidx/test/Snakefile
+++ b/bio/samtools/faidx/test/Snakefile
@@ -38,16 +38,31 @@ rule samtools_faidx_bgzip:
         "master/bio/samtools/faidx"
 
 
-rule samtools_faidx_region:
+rule samtools_faidx_region_file:
     input:
         "{sample}.fa",
         fai="idx/{sample}.fa.fai",
+        regions="{sample}.regions",
     output:
-        "out/{sample}.fas",
+        "out/{sample}.region_file.fas",
     log:
-        "{sample}.region.log",
+        "{sample}.region_file.log",
     params:
-        region="ref",
+        extra="--length 5",
+    wrapper:
+        "master/bio/samtools/faidx"
+
+
+rule samtools_faidx_region_array:
+    input:
+        "{sample}.fa",
+        fai="idx/{sample}.fa.fai",
+    output:
+        "out/{sample}.region_array.fas",
+    log:
+        "{sample}.region_array.log",
+    params:
+        region=["ref", "ref2"],
         extra="--length 5",
     wrapper:
         "master/bio/samtools/faidx"
@@ -59,9 +74,9 @@ rule samtools_faidx_bgzip_region:
         fai="idx/{sample}.fa.bgz.fai",
         gzi="idx/{sample}.fa.bgz.gzi",
     output:
-        "out/{sample}.bgz.fas",
+        "out/{sample}.region_bgzip.fas",
     log:
-        "{sample}.bgzip_region.log",
+        "{sample}.region_bgzip.log",
     params:
         region="ref",
         extra="--length 5",
diff --git a/bio/samtools/faidx/test/genome.regions b/bio/samtools/faidx/test/genome.regions
new file mode 100644
index 00000000000..6415016b862
--- /dev/null
+++ b/bio/samtools/faidx/test/genome.regions
@@ -0,0 +1 @@
+ref
diff --git a/bio/samtools/faidx/wrapper.py b/bio/samtools/faidx/wrapper.py
index 63e44abfa91..3a85b1e177c 100644
--- a/bio/samtools/faidx/wrapper.py
+++ b/bio/samtools/faidx/wrapper.py
@@ -17,10 +17,11 @@
 # Get regions (if present)
 regions = snakemake.input.get("regions", "")
 if regions:
-    regions = f"--regions-file {regions}"
+    regions = f"--region-file {regions}"
 
 region = snakemake.params.get("region", "")
 
+
 # Get FAI and GZI files
 if region or regions:
     fai = snakemake.input.get("fai", "")
diff --git a/test.py b/test.py
index 8ab245518f1..605462538c0 100644
--- a/test.py
+++ b/test.py
@@ -4242,8 +4242,9 @@ def test_samtools_faidx():
             "out/genome.named.fa.fai",
             "out/genome.fas.bgz.fai",
             "out/genome.fas.bgz.gzi",
-            "out/genome.fas",
-            "out/genome.bgz.fas",
+            "out/genome.region_file.fas",
+            "out/genome.region_array.fas",
+            "out/genome.region_bgzip.fas",
             "--use-conda",
             "-F",
         ],