Merge pull request #140 from sanger-tol/patch

Release 1.3.2
sanger-tol · Jan 14, 2025 · cb000aa · cb000aa
2 parents 4751ca5 + e0a2b35
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,19 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[1.3.1](https://github.com/sanger-tol/readmapping/releases/tag/1.3.0)] - Antipodean Opaleye (patch 1) - [2024-09-24]
+## [[1.3.2](https://github.com/sanger-tol/readmapping/releases/tag/1.3.2)] - Antipodean Opaleye (patch 2) - [2025-01-13]
+
+### Enhancements & fixes
+
+- Dependency version updates
+- Remove references to Anaconda channels
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `bbtools`  | 39.01       | 39.10       |
+| `samtools` | 1.20        | 1.21        |
+
+## [[1.3.1](https://github.com/sanger-tol/readmapping/releases/tag/1.3.1)] - Antipodean Opaleye (patch 1) - [2024-09-24]
 
 ### Enhancements & fixes
 

diff --git a/conf/base.config b/conf/base.config
@@ -29,15 +29,15 @@ process {
         time   = { check_max( 4.hour * task.attempt, 'time' ) }
     }
 
-    withName: 'SAMTOOLS_(COLLATETOFASTA|FILTERTOFASTQ|FIXMATE|FLAGSTAT|MARKDUP|MERGE|VIEW)' {
+    withName: 'SAMTOOLS_(COLLATETOFASTA|COLLATETOFASTQ|FILTERTOFASTQ|FIXMATE|FLAGSTAT|MARKDUP|MERGE|VIEW)' {
         time   = { check_max( 8.hour * task.attempt, 'time' ) }
     }
 
     withName: 'SAMTOOLS_(FLAGSTAT|IDXSTATS)' {
         memory = { check_max( 250.MB  * task.attempt, 'memory'  ) }
     }
 
-    withName: 'SAMTOOLS_(STATS|VIEW)' {
+    withName: 'SAMTOOLS_(STATS|VIEW|COLLATETOFASTQ)' {
         memory = { check_max( ((meta.datatype == "pacbio_clr" || meta.datatype == "ont") ? 2.GB : 1.GB) * task.attempt, 'memory'  ) }
     }
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -11,8 +11,9 @@
 */
 
 process {
-    withName: SAMTOOLS_FASTQ {
-        ext.args = '-F 0x200 -nt'
+    withName: SAMTOOLS_COLLATETOFASTQ {
+        ext.args   = { (params.use_work_dir_as_temp ? "-T." : "") }
+        ext.args2 = '-F 0x200 -nt'
     }
 
     withName: BBMAP_FILTERBYNAME {

diff --git a/modules.json b/modules.json
@@ -7,88 +7,84 @@
                 "nf-core": {
                     "bbmap/filterbyname": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
                         "installed_by": ["modules"]
                     },
                     "blast/blastn": {
                         "branch": "master",
-                        "git_sha": "583edaf97c9373a20df05a3b7be5a6677f9cd719",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "bwamem2/index": {
                         "branch": "master",
-                        "git_sha": "7081e04c18de9480948d34513a1c1e2d0fa9126d",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "bwamem2/mem": {
                         "branch": "master",
-                        "git_sha": "2201e21b09213f083832ac58e33353d410a6fde7",
+                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
                         "installed_by": ["modules"]
                     },
                     "crumble": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "82024cf6325d2ee194e7f056d841ecad2f6856e9",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "minimap2/align": {
                         "branch": "master",
-                        "git_sha": "a33ef9475558c6b8da08c5f522ddaca1ec810306",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
-                        "installed_by": ["modules"]
-                    },
-                    "samtools/fastq": {
-                        "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
                         "installed_by": ["modules"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
                         "installed_by": ["modules"]
                     },
                     "samtools/merge": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/samtools/merge/samtools-merge.diff"
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "1fe379cf6e6c1e6fa5e32bcbeefea0f1e874dac6",
+                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
                         "installed_by": ["modules"]
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "6c2309aaec566c0d44a6cf14d4b2d0c51afe2e91",
-                        "installed_by": ["modules"]
+                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/samtools/view/samtools-view.diff"
                     },
                     "seqkit/fq2fa": {
                         "branch": "master",
-                        "git_sha": "03fbf6c89e551bd8d77f3b751fb5c955f75b34c5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/local/samtools_collatetofasta.nf b/modules/local/samtools_collatetofasta.nf
@@ -2,10 +2,10 @@ process SAMTOOLS_COLLATETOFASTA {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::samtools=1.20"
+    conda "bioconda::samtools=1.21"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
-        'biocontainers/samtools:1.20--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
+        'biocontainers/samtools:1.21--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(input)

diff --git a/modules/local/samtools_collatetofastq.nf b/modules/local/samtools_collatetofastq.nf
@@ -0,0 +1,52 @@
+process SAMTOOLS_COLLATETOFASTQ {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "bioconda::samtools=1.21"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
+        'biocontainers/samtools:1.21--h50ea8bc_0' }"
+
+    input:
+    tuple val(meta), path(input)
+    val(interleave)
+
+    output:
+    tuple val(meta), path("*_{1,2}.fasta")      , optional:true, emit: fasta
+    tuple val(meta), path("*_interleaved.fasta"), optional:true, emit: interleaved
+    tuple val(meta), path("*_singleton.fasta")  , optional:true, emit: singleton
+    tuple val(meta), path("*_other.fasta")      , optional:true, emit: other
+    path  "versions.yml"                        , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args  = task.ext.args  ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def output = ( interleave && ! meta.single_end ) ? "> ${prefix}_interleaved.fasta" :
+        meta.single_end ? "-1 ${prefix}_1.fasta -s ${prefix}_singleton.fasta" :
+        "-1 ${prefix}_1.fasta -2 ${prefix}_2.fasta -s ${prefix}_singleton.fasta"
+    """
+    samtools collate \\
+        $args \\
+        -O \\
+        -u \\
+        -T ${prefix}.collate \\
+        --threads $task.cpus \\
+        ${input} \\
+    | \\
+    samtools \\
+        fastq \\
+        $args2 \\
+        --threads ${task.cpus-1} \\
+        -0 ${prefix}_other.fastq.gz \\
+        $output
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/samtools_filtertofastq.nf b/modules/local/samtools_filtertofastq.nf
@@ -2,10 +2,10 @@ process SAMTOOLS_FILTERTOFASTQ {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::samtools=1.20"
+    conda "bioconda::samtools=1.21"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
-        'biocontainers/samtools:1.20--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
+        'biocontainers/samtools:1.21--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(input), path(index)

diff --git a/modules/local/samtools_replaceheader.nf b/modules/local/samtools_replaceheader.nf
@@ -2,10 +2,10 @@ process SAMTOOLS_REHEADER {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::samtools=1.20"
+    conda "bioconda::samtools=1.21"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
-        'biocontainers/samtools:1.20--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
+        'biocontainers/samtools:1.21--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(file)

diff --git a/modules/local/samtools_sormadup.nf b/modules/local/samtools_sormadup.nf
@@ -4,10 +4,10 @@ process SAMTOOLS_SORMADUP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::samtools=1.20"
+    conda "bioconda::samtools=1.21"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
-        'biocontainers/samtools:1.20--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
+        'biocontainers/samtools:1.21--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(input)

diff --git a/modules/nf-core/bbmap/filterbyname/environment.yml b/modules/nf-core/bbmap/filterbyname/environment.yml
diff --git a/modules/nf-core/bbmap/filterbyname/main.nf b/modules/nf-core/bbmap/filterbyname/main.nf