Merge branch 'master' into vep_110

nf-core · Jul 21, 2023 · 19bd890 · 19bd890
2 parents c3c3045 + 27902a2
commit 19bd890
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diff --git a/modules/nf-core/cnvkit/access/main.nf b/modules/nf-core/cnvkit/access/main.nf
@@ -2,10 +2,10 @@ process CNVKIT_ACCESS {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1"
+    conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0':
-        'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0':
+        'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)

diff --git a/modules/nf-core/cnvkit/access/meta.yml b/modules/nf-core/cnvkit/access/meta.yml
@@ -55,3 +55,4 @@ output:
 
 authors:
   - "@adamrtalbot"
+  - "@priesgo"
diff --git a/modules/nf-core/cnvkit/antitarget/main.nf b/modules/nf-core/cnvkit/antitarget/main.nf
@@ -2,10 +2,10 @@ process CNVKIT_ANTITARGET {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1"
+    conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0':
-        'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0':
+        'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(targets)

diff --git a/modules/nf-core/cnvkit/antitarget/meta.yml b/modules/nf-core/cnvkit/antitarget/meta.yml
@@ -43,4 +43,6 @@ output:
       pattern: "versions.yml"
 
 authors:
+  - "@adamrtalbot"
+  - "@priesgo"
   - "@SusiJo"
diff --git a/modules/nf-core/cnvkit/batch/main.nf b/modules/nf-core/cnvkit/batch/main.nf
@@ -2,10 +2,10 @@ process CNVKIT_BATCH {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1"
+    conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:3bdd798e4b9aed6d3e1aaa1596c913a3eeb865cb-0' :
-        'biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:3bdd798e4b9aed6d3e1aaa1596c913a3eeb865cb-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:c94363856059151a2974dc501fb07a0360cc60a3-0' :
+        'biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:c94363856059151a2974dc501fb07a0360cc60a3-0' }"
 
     input:
     tuple val(meta), path(tumor), path(normal)

diff --git a/modules/nf-core/cnvkit/batch/meta.yml b/modules/nf-core/cnvkit/batch/meta.yml
@@ -77,10 +77,12 @@ output:
       description: File containing software versions
       pattern: "versions.yml"
 authors:
-  - "@kaurravneet4123"
-  - "@KevinMenden"
-  - "@MaxUlysse"
+  - "@adamrtalbot"
   - "@drpatelh"
   - "@fbdtemme"
+  - "@kaurravneet4123"
+  - "@KevinMenden"
   - "@lassefolkersen"
+  - "@MaxUlysse"
+  - "@priesgo"
   - "@SusiJo"
diff --git a/modules/nf-core/cnvkit/call/main.nf b/modules/nf-core/cnvkit/call/main.nf
@@ -2,10 +2,10 @@ process CNVKIT_CALL {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1"
+    conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0':
-        'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0':
+        'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
 
     input:
     tuple val(meta) , path(cns), path(vcf)

diff --git a/modules/nf-core/cnvkit/call/meta.yml b/modules/nf-core/cnvkit/call/meta.yml
@@ -2,6 +2,8 @@ name: cnvkit_call
 description: Given segmented log2 ratio estimates (.cns), derive each segment’s absolute integer copy number
 keywords:
   - cnvkit
+  - bam
+  - fasta
   - copy number
 tools:
   - cnvkit:
@@ -47,3 +49,4 @@ output:
 
 authors:
   - "@adamrtalbot"
+  - "@priesgo"
diff --git a/modules/nf-core/cnvkit/export/main.nf b/modules/nf-core/cnvkit/export/main.nf
@@ -2,10 +2,10 @@ process CNVKIT_EXPORT {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1"
+    conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0':
-        'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0':
+        'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
 
     input:
     tuple val(meta) , path(cns)

diff --git a/modules/nf-core/cnvkit/export/meta.yml b/modules/nf-core/cnvkit/export/meta.yml
@@ -43,3 +43,4 @@ output:
 
 authors:
   - "@adamrtalbot"
+  - "@priesgo"
diff --git a/modules/nf-core/cnvkit/genemetrics/main.nf b/modules/nf-core/cnvkit/genemetrics/main.nf
@@ -2,10 +2,10 @@ process CNVKIT_GENEMETRICS {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1"
+    conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0':
-        'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0':
+        'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(cnr), path(cns)

diff --git a/modules/nf-core/cnvkit/genemetrics/meta.yml b/modules/nf-core/cnvkit/genemetrics/meta.yml
@@ -2,7 +2,9 @@ name: cnvkit_genemetrics
 description: Copy number variant detection from high-throughput sequencing data
 keywords:
   - cnvkit
-  - genemetrics
+  - bam
+  - fasta
+  - copy number
 tools:
   - cnvkit:
       description: |
@@ -40,4 +42,6 @@ output:
       pattern: "versions.yml"
 
 authors:
+  - "@adamrtalbot"
   - "@marrip"
+  - "@priesgo"
diff --git a/modules/nf-core/cnvkit/reference/main.nf b/modules/nf-core/cnvkit/reference/main.nf
@@ -2,10 +2,10 @@ process CNVKIT_REFERENCE {
     tag "$fasta"
     label 'process_low'
 
-    conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1"
+    conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0':
-        'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0':
+        'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
 
     input:
     path fasta

diff --git a/modules/nf-core/cnvkit/reference/meta.yml b/modules/nf-core/cnvkit/reference/meta.yml
@@ -46,4 +46,6 @@ output:
       pattern: "versions.yml"
 
 authors:
+  - "@adamrtalbot"
+  - "@priesgo"
   - "@SusiJo"
diff --git a/modules/nf-core/cnvkit/target/main.nf b/modules/nf-core/cnvkit/target/main.nf
@@ -2,10 +2,10 @@ process CNVKIT_TARGET {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1"
+    conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0':
-        'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0':
+        'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(baits)

diff --git a/modules/nf-core/cnvkit/target/meta.yml b/modules/nf-core/cnvkit/target/meta.yml
@@ -58,3 +58,4 @@ output:
 
 authors:
   - "@adamrtalbot"
+  - "@priesgo"
diff --git a/modules/nf-core/gatk/indelrealigner/main.nf b/modules/nf-core/gatk/indelrealigner/main.nf
@@ -9,10 +9,10 @@ process GATK_INDELREALIGNER {
 
     input:
     tuple val(meta), path(bam), path(bai), path(intervals)
-    path(fasta)
-    path(fai)
-    path(dict)
-    path(known_vcf)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    tuple val(meta4), path(dict)
+    tuple val(meta5), path(known_vcf)
 
     output:
     tuple val(meta), path("*.bam"), path("*.bai"), emit: bam

diff --git a/modules/nf-core/gatk/indelrealigner/meta.yml b/modules/nf-core/gatk/indelrealigner/meta.yml
@@ -31,18 +31,38 @@ input:
       type: file
       description: Intervals file created by gatk3 RealignerTargetCreator
       pattern: "*.{intervals,list}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information.
+        e.g. [ id:'test', single_end:false ]
   - fasta:
       type: file
       description: Reference file used to generate BAM file
       pattern: ".{fasta,fa,fna}"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing reference information.
+        e.g. [ id:'test', single_end:false ]
   - fai:
       type: file
       description: Index of reference file used to generate BAM file
       pattern: ".fai"
+  - meta4:
+      type: map
+      description: |
+        Groovy Map containing reference information.
+        e.g. [ id:'test', single_end:false ]
   - dict:
       type: file
       description: GATK dict file for reference
       pattern: ".dict"
+  - meta5:
+      type: map
+      description: |
+        Groovy Map containing file meta-information for known_vcf.
+        e.g. [ id:'test', single_end:false ]
   - known_vcf:
       type: file
       description: Optional input VCF file(s) with known indels

diff --git a/modules/nf-core/gatk/realignertargetcreator/main.nf b/modules/nf-core/gatk/realignertargetcreator/main.nf
@@ -8,11 +8,11 @@ process GATK_REALIGNERTARGETCREATOR {
         'biocontainers/gatk:3.5--hdfd78af_11' }"
 
     input:
-    tuple val(meta), path(input), path(index)
-    path fasta
-    path fai
-    path dict
-    path known_vcf
+    tuple val(meta), path(bam), path(bai)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    tuple val(meta4), path(dict)
+    tuple val(meta5), path(known_vcf)
 
     output:
     tuple val(meta), path("*.intervals"), emit: intervals
@@ -25,7 +25,7 @@ process GATK_REALIGNERTARGETCREATOR {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def known = known_vcf ? "-known ${known_vcf}" : ""
-    if ("$input" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
 
     def avail_mem = 3072
     if (!task.memory) {
@@ -39,7 +39,7 @@ process GATK_REALIGNERTARGETCREATOR {
         -Xmx${avail_mem}M \\
         -T RealignerTargetCreator \\
         -nt ${task.cpus} \\
-        -I ${input} \\
+        -I ${bam} \\
         -R ${fasta} \\
         -o ${prefix}.intervals \\
         ${known} \\

diff --git a/modules/nf-core/gatk/realignertargetcreator/meta.yml b/modules/nf-core/gatk/realignertargetcreator/meta.yml
@@ -20,26 +20,46 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - input:
+  - bam:
       type: file
       description: Sorted and indexed BAM/CRAM/SAM file
       pattern: "*.bam"
-  - index:
+  - bai:
       type: file
       description: BAM index file
       pattern: "*.bai"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information.
+        e.g. [ id:'test', single_end:false ]
   - fasta:
       type: file
       description: Reference file used to generate BAM file
       pattern: ".{fasta,fa,fna}"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing reference information.
+        e.g. [ id:'test', single_end:false ]
   - fai:
       type: file
       description: Index of reference file used to generate BAM file
       pattern: ".fai"
+  - meta4:
+      type: map
+      description: |
+        Groovy Map containing reference information.
+        e.g. [ id:'test', single_end:false ]
   - dict:
       type: file
       description: GATK dict file for reference
       pattern: ".dict"
+  - meta5:
+      type: map
+      description: |
+        Groovy Map containing file meta-information for known_vcf.
+        e.g. [ id:'test', single_end:false ]
   - known_vcf:
       type: file
       description: Optional input VCF file(s) with known indels

diff --git a/modules/nf-core/gatk/unifiedgenotyper/main.nf b/modules/nf-core/gatk/unifiedgenotyper/main.nf
@@ -8,14 +8,14 @@ process GATK_UNIFIEDGENOTYPER {
         'biocontainers/gatk:3.5--hdfd78af_11' }"
 
     input:
-    tuple val(meta), path(input), path(index)
-    path  fasta
-    path  fai
-    path  dict
-    path  intervals
-    path  contamination
-    path  dbsnp
-    path  comp
+    tuple val(meta), path(bam), path(bai)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    tuple val(meta4), path(dict)
+    tuple val(meta5), path(intervals)
+    tuple val(meta6), path(contamination)
+    tuple val(meta7), path(dbsnp)
+    tuple val(meta8), path(comp)
 
     output:
     tuple val(meta), path("*.vcf.gz"), emit: vcf
@@ -44,7 +44,7 @@ process GATK_UNIFIEDGENOTYPER {
         -Xmx${avail_mem}M \\
         -nt ${task.cpus} \\
         -T UnifiedGenotyper \\
-        -I ${input} \\
+        -I ${bam} \\
         -R ${fasta} \\
         ${contamination_file} \\
         ${dbsnp_file} \\