Merge branch 'nf-core:master' into master

adamrtalbot · Sep 21, 2023 · 3793e04 · 3793e04
2 parents 655d729 + 121b2d7
commit 3793e04
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -193,6 +193,8 @@ jobs:
             tags: merquryfk/merquryfk
           - profile: "conda"
             tags: merquryfk/ploidyplot
+          - profile: "conda"
+            tags: mitohifi/mitohifi
           - profile: "conda"
             tags: mitohifi/findmitoreference
           - profile: "conda"

diff --git a/modules/nf-core/bamcmp/main.nf b/modules/nf-core/bamcmp/main.nf
@@ -8,26 +8,37 @@ process BAMCMP {
         'biocontainers/bamcmp:2.2--h05f6578_0' }"
 
     input:
-    tuple val(meta), path(sample), path(contaminant)
+    tuple val(meta), path(primary_aligned_bam), path(contaminant_aligned_bam)
 
     output:
-    tuple val(meta), path("*primary.bam")      , emit: bam
-    tuple val(meta), path("*contamination.bam"), emit: contamination_bam
-    path "versions.yml"                        , emit: versions
+    tuple val(meta), path("${prefix}.bam") , emit: primary_filtered_bam
+    tuple val(meta), path("${prefix2}.bam"), emit: contamination_bam
+    path "versions.yml"                    , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}_primary"
+    prefix2 = task.ext.prefix2 ?: "${meta.id}_contaminant"
+
+    if ("$primary_aligned_bam" == "${prefix}.bam"  | "$contaminant_aligned_bam" == "${prefix}.bam"  )
+        error "Input and output names for the primary-genome bam file are the same, use \"task.ext.prefix\" to disambiguate!"
+    if ("$primary_aligned_bam" == "${prefix2}.bam" | "$contaminant_aligned_bam" == "${prefix2}.bam" )
+        error "Input and output names for the contaminant-genome bam file are the same, use \"task.ext.prefix2\" to disambiguate!"
+    if ("primary_aligned_bam"    == "contaminant_aligned_bam" )
+        error "Input file names for the two bam files are the same, ensure they are renamed upstream."
+    if ("${prefix}.bam"    == "${prefix2}.bam" )
+        error "Output names for the two bam files are identical, use \"task.ext.prefix\" and \"task.ext.prefix2\" to disambiguate!"
+
     def VERSION = '2.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     bamcmp \\
-        -1 $sample \\
-        -2 $contaminant \\
-        -A ${prefix}_primary.bam \\
-        -B ${prefix}_contamination.bam \\
+        -1 $primary_aligned_bam \\
+        -2 $contaminant_aligned_bam \\
+        -A ${prefix}.bam \\
+        -B ${prefix2}.bam \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
@@ -36,4 +47,27 @@ process BAMCMP {
     END_VERSIONS
     """
 
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}_primary"
+    prefix2 = task.ext.prefix2 ?: "${meta.id}_contaminant"
+
+    if ("$primary_aligned_bam" == "${prefix}.bam"  | "$contaminant_aligned_bam" == "${prefix}.bam"  )
+        error "Input and output names for the primary-genome bam file are the same, use \"task.ext.prefix\" to disambiguate!"
+    if ("$primary_aligned_bam" == "${prefix2}.bam" | "$contaminant_aligned_bam" == "${prefix2}.bam" )
+        error "Input and output names for the contaminant-genome bam file are the same, use \"task.ext.prefix2\" to disambiguate!"
+    if ("primary_aligned_bam"    == "contaminant_aligned_bam" )
+        error "Input file names for the two bam files are the same, ensure they are renamed upstream."
+    if ("${prefix}.bam"    == "${prefix2}.bam" )
+        error "Output names for the two bam files are identical, use \"task.ext.prefix\" and \"task.ext.prefix2\" to disambiguate!"
+    """
+    touch ${prefix}.bam
+    touch ${prefix2}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ngscheckmate: \$(ncm.py --help | sed "7!d;s/ *Ensuring Sample Identity v//g")
+    END_VERSIONS
+    """
+
 }
diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf
@@ -9,7 +9,7 @@ process BCFTOOLS_MPILEUP {
 
     input:
     tuple val(meta), path(bam), path(intervals)
-    path fasta
+    tuple val(meta2), path(fasta)
     val save_mpileup
 
     output:

diff --git a/modules/nf-core/bcftools/mpileup/meta.yml b/modules/nf-core/bcftools/mpileup/meta.yml
@@ -25,6 +25,10 @@ input:
   - intervals:
       type: file
       description: Input intervals file. A file (commonly '.bed') containing regions to subset
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing information about the genome fasta, e.g. [ id: 'sarscov2' ]
   - fasta:
       type: file
       description: FASTA reference file

diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf
@@ -30,6 +30,7 @@ process BCFTOOLS_SORT {
     bcftools \\
         sort \\
         --output ${prefix}.${extension} \\
+        --temp-dir . \\
         $args \\
         $vcf
 

diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf
@@ -18,13 +18,14 @@ process BWA_INDEX {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${fasta.baseName}"
+    def args   = task.ext.args ?: ''
     """
     mkdir bwa
     bwa \\
         index \\
         $args \\
-        -p bwa/${fasta.baseName} \\
+        -p bwa/${prefix} \\
         $fasta
 
     cat <<-END_VERSIONS > versions.yml
@@ -34,14 +35,15 @@ process BWA_INDEX {
     """
 
     stub:
+    def prefix = task.ext.prefix ?: "${fasta.baseName}"
     """
     mkdir bwa
 
-    touch bwa/genome.amb
-    touch bwa/genome.ann
-    touch bwa/genome.bwt
-    touch bwa/genome.pac
-    touch bwa/genome.sa
+    touch bwa/${prefix}.amb
+    touch bwa/${prefix}.ann
+    touch bwa/${prefix}.bwt
+    touch bwa/${prefix}.pac
+    touch bwa/${prefix}.sa
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf
@@ -18,13 +18,14 @@ process BWAMEM2_INDEX {
     task.ext.when == null || task.ext.when
 
     script:
+    def prefix = task.ext.prefix ?: "${fasta}"
     def args = task.ext.args ?: ''
     """
     mkdir bwamem2
     bwa-mem2 \\
         index \\
         $args \\
-        $fasta -p bwamem2/${fasta}
+        $fasta -p bwamem2/${prefix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -33,13 +34,15 @@ process BWAMEM2_INDEX {
     """
 
     stub:
+    def prefix = task.ext.prefix ?: "${fasta}"
+
     """
     mkdir bwamem2
-    touch bwamem2/${fasta}.0123
-    touch bwamem2/${fasta}.ann
-    touch bwamem2/${fasta}.pac
-    touch bwamem2/${fasta}.amb
-    touch bwamem2/${fasta}.bwt.2bit.64
+    touch bwamem2/${prefix}.0123
+    touch bwamem2/${prefix}.ann
+    touch bwamem2/${prefix}.pac
+    touch bwamem2/${prefix}.amb
+    touch bwamem2/${prefix}.bwt.2bit.64
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/cnvkit/batch/main.nf b/modules/nf-core/cnvkit/batch/main.nf
@@ -9,10 +9,10 @@ process CNVKIT_BATCH {
 
     input:
     tuple val(meta), path(tumor), path(normal)
-    path  fasta
-    path  fasta_fai
-    path  targets
-    path  reference
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fasta_fai)
+    tuple val(meta4), path(targets)
+    tuple val(meta5), path(reference)
     val   panel_of_normals
 
     output:

diff --git a/modules/nf-core/cnvkit/batch/meta.yml b/modules/nf-core/cnvkit/batch/meta.yml
@@ -26,22 +26,43 @@ input:
       type: file
       description: |
         Input normal sample bam file (or cram)
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
   - fasta:
       type: file
       description: |
         Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided)
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
   - fasta_fai:
       type: file
       description: |
         Input reference genome fasta index (optional, but recommended for cram_input)
+  - meta4:
+      type: map
+      description: |
+        Groovy Map containing information about target file
+        e.g. [ id:'test' ]
   - targetfile:
       type: file
       description: |
         Input target bed file
+  - meta5:
+      type: map
+      description: |
+        Groovy Map containing information about reference file
+        e.g. [ id:'test' ]
   - reference:
       type: file
       description: |
         Input reference cnn-file (only for germline and tumor-only running)
+
 output:
   - meta:
       type: map
@@ -76,6 +97,7 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
+
 authors:
   - "@adamrtalbot"
   - "@drpatelh"

diff --git a/modules/nf-core/controlfreec/assesssignificance/main.nf b/modules/nf-core/controlfreec/assesssignificance/main.nf
@@ -2,10 +2,10 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::control-freec=11.6"
+    conda "bioconda::control-freec=11.6b"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
-        'biocontainers/control-freec:11.6--h1b792b2_1' }"
+        'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0 ':
+        'biocontainers/control-freec:11.6b--hdbdd923_0 ' }"
 
     input:
     tuple val(meta), path(cnvs), path(ratio)

diff --git a/modules/nf-core/controlfreec/freec/main.nf b/modules/nf-core/controlfreec/freec/main.nf
@@ -2,10 +2,10 @@ process CONTROLFREEC_FREEC {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::control-freec=11.6"
+    conda "bioconda::control-freec=11.6b"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
-        'biocontainers/control-freec:11.6--h1b792b2_1' }"
+        'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0 ':
+        'biocontainers/control-freec:11.6b--hdbdd923_0 ' }"
 
     input:
     tuple val(meta), path(mpileup_normal), path(mpileup_tumor), path(cpn_normal), path(cpn_tumor), path(minipileup_normal), path(minipileup_tumor)

diff --git a/modules/nf-core/controlfreec/freec2bed/main.nf b/modules/nf-core/controlfreec/freec2bed/main.nf
@@ -2,10 +2,10 @@ process CONTROLFREEC_FREEC2BED {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::control-freec=11.6"
+    conda "bioconda::control-freec=11.6b"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
-        'biocontainers/control-freec:11.6--h1b792b2_1' }"
+        'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0 ':
+        'biocontainers/control-freec:11.6b--hdbdd923_0 ' }"
 
     input:
     tuple val(meta), path(ratio)

diff --git a/modules/nf-core/controlfreec/freec2circos/main.nf b/modules/nf-core/controlfreec/freec2circos/main.nf
@@ -2,10 +2,10 @@ process CONTROLFREEC_FREEC2CIRCOS {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::control-freec=11.6"
+    conda "bioconda::control-freec=11.6b"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
-        'biocontainers/control-freec:11.6--h1b792b2_1' }"
+        'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0 ':
+        'biocontainers/control-freec:11.6b--hdbdd923_0 ' }"
 
     input:
     tuple val(meta), path(ratio)

diff --git a/modules/nf-core/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf
@@ -2,11 +2,10 @@ process CONTROLFREEC_MAKEGRAPH {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::control-freec=11.6"
+    conda "bioconda::control-freec=11.6b"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
-        'biocontainers/control-freec:11.6--h1b792b2_1' }"
-
+        'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0 ':
+        'biocontainers/control-freec:11.6b--hdbdd923_0 ' }"
     input:
     tuple val(meta), path(ratio), path(baf), val(ploidy)
 

diff --git a/modules/nf-core/csvtk/join/main.nf b/modules/nf-core/csvtk/join/main.nf
@@ -0,0 +1,50 @@
+process CSVTK_JOIN {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "bioconda::csvtk=0.26.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/csvtk:0.26.0--h9ee0642_0':
+        'biocontainers/csvtk:0.26.0--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(csv)
+
+    output:
+    tuple val(meta), path("${prefix}.${out_extension}"), emit: csv
+    path "versions.yml"                                , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    out_extension = args.contains('--out-delimiter "\t"') || args.contains('-D "\t"') || args.contains("-D \$'\t'") ? "tsv" : "csv"
+    """
+    csvtk \\
+        join \\
+        $args \\
+        --num-cpus $task.cpus \\
+        --out-file ${prefix}.${out_extension} \\
+        $csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        csvtk: \$(echo \$( csvtk version | sed -e "s/csvtk v//g" ))
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    out_extension = args.contains('--out-delimiter "\t"') || args.contains('-D "\t"') || args.contains("-D \$'\t'") ? "tsv" : "csv"
+    """
+    touch ${prefix}.${out_extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        csvtk: \$(echo \$( csvtk version | sed -e "s/csvtk v//g" ))
+    END_VERSIONS
+    """
+}