Merge branch 'master' into aria2c

snakemake · Jun 6, 2024 · bb9e70d · bb9e70d
2 parents 2fb58b2 + 1e9e511
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diff --git 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)
 
 

diff --git 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
@@ -3,6 +3,6 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bowtie2 =2.5.3
+  - bowtie2 =2.5.4
   - bismark =0.24.2
   - samtools =1.20