Update versions (#1292)

* Update versions

* update checksums + remove variables as input for applyvqsr

* sneak in removal of values and provide them via modules.config

* update another checksum

* more checksums

* move vairable to config

* remove controlfreec, wrong branch

* add line break

modules/gatk4/applybqsr/main.nf

@@ -2,10 +2,10 @@ process GATK4_APPLYBQSR {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)

modules/gatk4/applyvqsr/main.nf

@@ -2,19 +2,16 @@ process GATK4_APPLYVQSR {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi), path(recal), path(recalidx), path(tranches)
     path fasta
     path fai
     path dict
-    val allelespecific
-    val truthsensitivity
-    val mode
 
     output:
     tuple val(meta), path("*.vcf.gz")     , emit: vcf
@@ -28,9 +25,6 @@ process GATK4_APPLYVQSR {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     refCommand = fasta ? "-R ${fasta} " : ''
-    alleleSpecificCommand = allelespecific ? '-AS' : ''
-    truthSensitivityCommand = truthsensitivity ? "--truth-sensitivity-filter-level ${truthsensitivity}" : ''
-    modeCommand = mode ? "--mode ${mode} " : 'SNP'
 
     def avail_mem = 3
     if (!task.memory) {
@@ -43,11 +37,8 @@ process GATK4_APPLYVQSR {
         ${refCommand} \\
         -V ${vcf} \\
         -O ${prefix}.vcf.gz \\
-        ${alleleSpecificCommand} \\
-        ${truthSensitivityCommand} \\
         --tranches-file $tranches \\
         --recal-file $recal \\
-        ${modeCommand} \\
         $args
 
     cat <<-END_VERSIONS > versions.yml

modules/gatk4/applyvqsr/meta.yml

@@ -57,18 +57,6 @@ input:
       type: file
       description: GATK sequence dictionary
       pattern: "*.dict"
-  - allelespecific:
-      type: boolean
-      description: Whether or not to run ApplyVQSR in allele specific mode, this should be kept the same as the stage 1 VariantRecalibrator run.
-      pattern: "{true,false}"
-  - truthsensitivity:
-      type: double
-      description: Value to be used as the truth sensitivity cutoff score.
-      pattern: "99.0"
-  - mode:
-      type: String
-      description: Specifies which recalibration mode to employ, should be the same as the stage 1 VariantRecalibrator run. (SNP is default, BOTH is intended for testing only)
-      pattern: "{SNP,INDEL,BOTH}"
 
 output:
   - vcf:

modules/gatk4/baserecalibrator/main.nf

@@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals)

modules/gatk4/bedtointervallist/main.nf

@@ -2,10 +2,10 @@ process GATK4_BEDTOINTERVALLIST {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bed)

modules/gatk4/calculatecontamination/main.nf

@@ -2,10 +2,10 @@ process GATK4_CALCULATECONTAMINATION {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(pileup), path(matched)

modules/gatk4/createsequencedictionary/main.nf

@@ -2,10 +2,10 @@ process GATK4_CREATESEQUENCEDICTIONARY {
     tag "$fasta"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     path fasta

modules/gatk4/createsomaticpanelofnormals/main.nf

@@ -2,10 +2,10 @@ process GATK4_CREATESOMATICPANELOFNORMALS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(genomicsdb)

modules/gatk4/estimatelibrarycomplexity/main.nf

@@ -2,10 +2,10 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(cram)

modules/gatk4/fastqtosam/main.nf

@@ -2,10 +2,10 @@ process GATK4_FASTQTOSAM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)

modules/gatk4/filtermutectcalls/main.nf

@@ -2,10 +2,10 @@ process GATK4_FILTERMUTECTCALLS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi), path(stats), path(orientationbias), path(segmentation), path(contaminationfile), val(contaminationest)

modules/gatk4/gatherbqsrreports/main.nf

@@ -2,10 +2,10 @@ process GATK4_GATHERBQSRREPORTS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(recal_table)

modules/gatk4/genomicsdbimport/main.nf

@@ -2,10 +2,10 @@ process GATK4_GENOMICSDBIMPORT {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi), path(intervalfile), val(intervalval), path(wspace)

modules/gatk4/genotypegvcfs/main.nf

@@ -2,10 +2,10 @@ process GATK4_GENOTYPEGVCFS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gvcf), path(gvcf_index), path(intervals)

modules/gatk4/getpileupsummaries/main.nf

@@ -2,10 +2,10 @@ process GATK4_GETPILEUPSUMMARIES {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(index), path(intervals)

modules/gatk4/haplotypecaller/main.nf

@@ -2,10 +2,10 @@ process GATK4_HAPLOTYPECALLER {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals)

modules/gatk4/indexfeaturefile/main.nf

@@ -2,10 +2,10 @@ process GATK4_INDEXFEATUREFILE {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(feature_file)

modules/gatk4/intervallisttools/main.nf

@@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOOLS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(interval_list)

modules/gatk4/learnreadorientationmodel/main.nf

@@ -2,10 +2,10 @@ process GATK4_LEARNREADORIENTATIONMODEL {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(f1r2)

modules/gatk4/markduplicates/main.nf

@@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bams)

modules/gatk4/mergebamalignment/main.nf

@@ -2,10 +2,10 @@ process GATK4_MERGEBAMALIGNMENT {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(aligned), path(unmapped)

modules/gatk4/mergevcfs/main.nf

@@ -2,10 +2,10 @@ process GATK4_MERGEVCFS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcfs)

modules/gatk4/mutect2/main.nf

@@ -2,10 +2,10 @@ process GATK4_MUTECT2 {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta) , path(input) , path(input_index) , path(intervals), val(which_norm)

modules/gatk4/revertsam/main.nf

@@ -2,10 +2,10 @@ process GATK4_REVERTSAM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/gatk4/samtofastq/main.nf

@@ -2,10 +2,10 @@ process GATK4_SAMTOFASTQ {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/gatk4/splitncigarreads/main.nf

@@ -2,10 +2,10 @@ process GATK4_SPLITNCIGARREADS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/gatk4/variantfiltration/main.nf

@@ -2,10 +2,10 @@ process GATK4_VARIANTFILTRATION {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(vcf_tbi)

modules/gatk4/variantrecalibrator/main.nf

@@ -2,21 +2,17 @@ process GATK4_VARIANTRECALIBRATOR {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf) , path(tbi)
     path fasta
     path fai
     path dict
-    val allelespecific
     tuple path(resvcfs), path(restbis), val(reslabels)
-    val annotation
-    val mode
-    val create_rscript
 
     output:
     tuple val(meta), path("*.recal")   , emit: recal
@@ -32,11 +28,7 @@ process GATK4_VARIANTRECALIBRATOR {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     refCommand = fasta ? "-R ${fasta} " : ''
-    alleleSpecificCommand = allelespecific ? '-AS' : ''
     resourceCommand = '--resource:' + reslabels.join( ' --resource:')
-    annotationCommand = '-an ' + annotation.join( ' -an ')
-    modeCommand = mode ? "--mode ${mode} " : 'SNP'
-    rscriptCommand = create_rscript ? "--rscript-file ${prefix}.plots.R" : ''
 
     def avail_mem = 3
     if (!task.memory) {
@@ -48,13 +40,9 @@ process GATK4_VARIANTRECALIBRATOR {
     gatk --java-options "-Xmx${avail_mem}g" VariantRecalibrator \\
         ${refCommand} \\
         -V ${vcf} \\
-        ${alleleSpecificCommand} \\
-        ${resourceCommand} \\
-        ${annotationCommand} \\
-        ${modeCommand} \\
         -O ${prefix}.recal \\
         --tranches-file ${prefix}.tranches \\
-        ${rscriptCommand}\\
+        ${resourceCommand} \\
         $args
 
     cat <<-END_VERSIONS > versions.yml

modules/gatk4/variantrecalibrator/meta.yml

@@ -45,10 +45,6 @@ input:
       type: file
       description: GATK sequence dictionary
       pattern: "*.dict"
-  - allelespecific:
-      type: boolean
-      description: specify whether to use allele specific annotations
-      pattern: "{true,false}"
   - resvcfs:
       type: list
       description: resource files to be used as truth, training and known sites resources, this imports the files into the module, file names are specified again in the resource_labels to be called via the command.
@@ -57,22 +53,6 @@ input:
       type: list
       description: tbis for the corresponding vcfs files to be used as truth, training and known resources.
       pattern: '*/hapmap_3.3.hg38_chr21.vcf.gz.tbi'
-  - reslabels:
-      type: list
-      description: labels for the resource files to be used as truth, training and known sites resources, label should include an identifier,which kind of resource(s) it is, prior value and name of the file.
-      pattern: "hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38_chr21.vcf.gz"
-  - annotation:
-      type: list
-      description: specify which annotations should be used for calculations.
-      pattern: "['QD', 'MQ', 'FS', 'SOR']"
-  - mode:
-      type: string
-      description: specifies which recalibration mode to employ (SNP is default, BOTH is intended for testing only)
-      pattern: "{SNP,INDEL,BOTH}"
-  - rscript:
-      type: boolean
-      description: specify whether to generate rscript.plot output file
-      pattern: "{true,false}"
 output:
   - recal:
       type: file

tests/modules/gatk4/applybqsr/test.yml

@@ -5,9 +5,9 @@
     - gatk4/applybqsr
   files:
     - path: output/gatk4/test.bam
-      md5sum: 908825edf1f229a072f91d8b753d95dd
+      md5sum: d088422be886dc8507ff97fcc7dd968a
     - path: output/gatk4/versions.yml
-      md5sum: b65c46529ae9658db0c596cbc26505c2
+      md5sum: d5c6455d8a77aecc63f87c795fc3443e
 
 - name: gatk4 applybqsr test_gatk4_applybqsr_intervals
   command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config
@@ -16,9 +16,9 @@
     - gatk4/applybqsr
   files:
     - path: output/gatk4/test.bam
-      md5sum: 50f8a79c7d528e02470416f81eb582bc
+      md5sum: 4bfa18d651abd945e240b05e70107716
     - path: output/gatk4/versions.yml
-      md5sum: 17c8a40b3537e3400edebd1826d28385
+      md5sum: cb4cb8a62e117b4adc643ae47883d53c
 
 - name: gatk4 applybqsr test_gatk4_applybqsr_cram
   command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_cram -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config
@@ -27,6 +27,6 @@
     - gatk4/applybqsr
   files:
     - path: output/gatk4/test.cram
-      md5sum: cd8d4ba6181f714e74641adeb2f9aa1d
+      md5sum: 2e0bca197af4f043a4a85152e6edbe04
     - path: output/gatk4/versions.yml
-      md5sum: 35218922e1929c699ea64de9f4c29fb5
+      md5sum: 1efaa18be943bab4e4c54191d6eaa260

tests/modules/gatk4/applyvqsr/main.nf

@@ -2,7 +2,8 @@
 
 nextflow.enable.dsl = 2
 
-include { GATK4_APPLYVQSR } from '../../../../modules/gatk4/applyvqsr/main.nf'
+include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_NO_ALLELSPECIFICITY } from '../../../../modules/gatk4/applyvqsr/main.nf'
+include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_WITH_ALLELSPECIFICITY} from '../../../../modules/gatk4/applyvqsr/main.nf'
 
 workflow test_gatk4_applyvqsr {
     input = [ [ id:'test'], // meta map
@@ -15,11 +16,8 @@ workflow test_gatk4_applyvqsr {
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
     fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
     dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-    allelespecific = false
-    truthsensitivity = '99.0'
-    mode = 'SNP'
 
-    GATK4_APPLYVQSR ( input, fasta, fai, dict, allelespecific, truthsensitivity, mode )
+    GATK4_APPLYVQSR_NO_ALLELSPECIFICITY ( input, fasta, fai, dict )
 }
 
 workflow test_gatk4_applyvqsr_allele_specific {
@@ -33,9 +31,6 @@ workflow test_gatk4_applyvqsr_allele_specific {
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
     fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
     dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-    allelespecific = true
-    truthsensitivity = '99.0'
-    mode = 'SNP'
 
-    GATK4_APPLYVQSR ( input, fasta, fai, dict, allelespecific, truthsensitivity, mode )
+    GATK4_APPLYVQSR_WITH_ALLELSPECIFICITY ( input, fasta, fai, dict)
 }

tests/modules/gatk4/applyvqsr/nextflow.config

@@ -1,5 +1,11 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
+    withName: GATK4_APPLYVQSR_NO_ALLELSPECIFICITY {
+        ext.args = '--mode SNP --truth-sensitivity-filter-level 99.0'
+    }
+
+    withName: GATK4_APPLYVQSR_WITH_ALLELSPECIFICITY {
+        ext.args = '--mode SNP --truth-sensitivity-filter-level 99.0 -AS'
+    }
 }

tests/modules/gatk4/applyvqsr/test.yml

@@ -7,7 +7,7 @@
     - path: output/gatk4/test.vcf.gz
     - path: output/gatk4/test.vcf.gz.tbi
     - path: output/gatk4/versions.yml
-      md5sum: 524a78cdfa56c8b09a4ff3f4cb278261
+      md5sum: ce9c443375683e7f2958fe958759ad29
 
 - name: gatk4 applyvqsr test_gatk4_applyvqsr_allele_specific
   command: nextflow run tests/modules/gatk4/applyvqsr -entry test_gatk4_applyvqsr_allele_specific -c tests/config/nextflow.config -c ./tests/modules/gatk4/applyvqsr/nextflow.config
@@ -18,4 +18,4 @@
     - path: output/gatk4/test.vcf.gz
     - path: output/gatk4/test.vcf.gz.tbi
     - path: output/gatk4/versions.yml
-      md5sum: 7a3c6e97628bd1f5f4e7fd429bf74a8e
+      md5sum: 521353d12d576de2864f1d18a3e54f14

tests/modules/gatk4/calculatecontamination/test.yml

@@ -7,7 +7,7 @@
     - path:  output/gatk4/test.contamination.table
       md5sum: 46c708c943b453da89a3da08acfdb2a7
     - path:  output/gatk4/versions.yml
-      md5sum: 79575dc2e6a7f0361f2d8b090c496070
+      md5sum: 3da8f1c0de968886330a3f7a3a1c6616
 
 - name: gatk4 calculatecontamination test_gatk4_calculatecontamination_matched_pair
   command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_matched_pair -c tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config
@@ -18,7 +18,7 @@
     - path:  output/gatk4/test.contamination.table
       md5sum: 46c708c943b453da89a3da08acfdb2a7
     - path:  output/gatk4/versions.yml
-      md5sum: 733f15ef7eb504daec9fd8cd9beef71a
+      md5sum: 14ab12a71b0c2b87d8cd53639a991b3a
 
 - name: gatk4 calculatecontamination test_gatk4_calculatecontamination_segmentation
   command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_segmentation -c tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config
@@ -31,4 +31,4 @@
     - path:  output/gatk4/test.segmentation.table
       md5sum: f4643d9319bde4efbfbe516d6fb13052
     - path:  output/gatk4/versions.yml
-      md5sum: 5396e33146addbe4a59d0f30cb573a3a
+      md5sum: d2e61315de31f512e448f0cb4b77db54

tests/modules/gatk4/fastqtosam/test.yml

@@ -6,7 +6,7 @@
   files:
     - path: output/gatk4/test.bam
     - path: output/gatk4/versions.yml
-      md5sum: 03f3accdc3e3c392c1179213286a0b67
+      md5sum: 381cdb2496b2fcc7bbc371a6e4156c7e
 
 - name: gatk4 fastqtosam test_gatk4_fastqtosam_paired_end
   command: nextflow run tests/modules/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c tests/config/nextflow.config  -c ./tests/modules/gatk4/fastqtosam/nextflow.config
@@ -16,4 +16,4 @@
   files:
     - path: output/gatk4/test.bam
     - path: output/gatk4/versions.yml
-      md5sum: 144e7118d5f277ad5fba863213c810b0
+      md5sum: 1d07c90cbd31992c9ba003f02d1b3502

tests/modules/gatk4/gatherbqsrreports/test.yml

@@ -7,7 +7,7 @@
     - path: output/gatk4/test.table
       md5sum: 9603b69fdc3b5090de2e0dd78bfcc4bf
     - path: output/gatk4/versions.yml
-      md5sum: b53101f71b0763e80855703ba4e1f101
+      md5sum: 8d52c5aaab73294e9ea5491b95f3e1e1
 
 - name: gatk4 gatherbqsrreports test_gatk4_gatherbqsrreports_multiple
   command: nextflow run tests/modules/gatk4/gatherbqsrreports -entry test_gatk4_gatherbqsrreports_multiple -c tests/config/nextflow.config
@@ -18,4 +18,4 @@
     - path: output/gatk4/test.table
       md5sum: 0c1257eececf95db8ca378272d0f21f9
     - path: output/gatk4/versions.yml
-      md5sum: 584a6ebf04f54abcfcf4c8255e13ff2a
+      md5sum: 91cad396b9f2045c3cd8c0f256672e80

tests/modules/gatk4/genomicsdbimport/test.yml

@@ -19,7 +19,7 @@
     - path: output/gatk4/test/vidmap.json
       md5sum: 18d3f68bd2cb6f4474990507ff95017a
     - path: output/gatk4/versions.yml
-      md5sum: 6fffaf981f099659cf820277d1f3c606
+      md5sum: 91f5c3e9529982f9c819860b403576ce
 
 - name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_get_intervalslist
   command: nextflow run tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_get_intervalslist -c tests/config/nextflow.config -c ./tests/modules/gatk4/genomicsdbimport/nextflow.config
@@ -30,7 +30,7 @@
     - path: output/gatk4/test.interval_list
       md5sum: 4c85812ac15fc1cd29711a851d23c0bf
     - path: output/gatk4/versions.yml
-      md5sum: 4a56022d6e08d54e8ba853637bf3b5f1
+      md5sum: a898fe1cbc4acfa5936c0ffdcf121401
     - path: output/untar/versions.yml
       md5sum: 8f080677b109aea2cfca50208b077534
 
@@ -55,6 +55,6 @@
     - path: output/gatk4/test_genomicsdb/vidmap.json
       md5sum: 18d3f68bd2cb6f4474990507ff95017a
     - path: output/gatk4/versions.yml
-      md5sum: da6a815b7340683b1a56bdfd7e66d463
+      md5sum: d87baa3f4218c5554cad3c008cb6cbc4
     - path: output/untar/versions.yml
       md5sum: 9b2916aea9790bdf427c0cb38109110c

tests/modules/gatk4/getpileupsummaries/test.yml

@@ -7,7 +7,7 @@
     - path: output/gatk4/test.pileups.table
       md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
     - path:  output/gatk4/versions.yml
-      md5sum: dd98374e3b5d35ddd1c6b3fa7e662dc5
+      md5sum: 059123619f3ed8d4cd178c4390b81e69
 
 - name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites
   command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c tests/config/nextflow.config
@@ -18,7 +18,7 @@
     - path:  output/gatk4/test.pileups.table
       md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
     - path:  output/gatk4/versions.yml
-      md5sum: 080b6af7df182558aeab117668388d59
+      md5sum: 76b5388b0c5b5762d8d33e34b23f181d
 
 - name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites_cram
   command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites_cram -c tests/config/nextflow.config
@@ -29,4 +29,4 @@
     - path:  output/gatk4/test.pileups.table
       md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
     - path:  output/gatk4/versions.yml
-      md5sum: 33458a9efa6d61c713af9f7b722d7134
+      md5sum: 2fa51319c2b1d678ee00ab09512cf268

tests/modules/gatk4/indexfeaturefile/test.yml

@@ -15,7 +15,7 @@
     - path: output/gatk4/genome.bed.gz.tbi
       md5sum: 4bc51e2351a6e83f20e13be75861f941
     - path: output/gatk4/versions.yml
-      md5sum: 9eb24dc17c96971b7991b3e154279aa7
+      md5sum: e5003204702f83aabdb4141272c704d2
 
 - name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf
   command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf -c tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config
@@ -25,7 +25,7 @@
   files:
     - path: output/gatk4/test.genome.vcf.idx
     - path: output/gatk4/versions.yml
-      md5sum: f76543e715342bf1fcdeb20385e01fe9
+      md5sum: 08cd7c49cfb752fc2905f600106a0345
 
 - name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf_gz
   command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf_gz -c tests/config/nextflow.config
@@ -36,4 +36,4 @@
     - path: output/gatk4/test.genome.vcf.gz.tbi
       md5sum: fedd68eaddf8d31257853d9da8325bd3
     - path: output/gatk4/versions.yml
-      md5sum: a5d988cf62648f700ffac7257e72b2c0
+      md5sum: b388d1681831a40264a7a27f67a8b247

tests/modules/gatk4/markduplicates/test.yml

@@ -5,12 +5,12 @@
     - gatk4/markduplicates
   files:
     - path: output/gatk4/test.bai
-      md5sum: c8f7a9e426c768577f88f59cb1336bf3
+      md5sum: e9c125e82553209933883b4fe2b8d7c2
     - path: output/gatk4/test.bam
-      md5sum: fba0c99a0b087c90113a210e4465f91b
+      md5sum: 2efd50b2e6b7fd9bdf242cd9e266cfa9
     - path: output/gatk4/test.metrics
     - path: output/gatk4/versions.yml
-      md5sum: dacbab0e112d2403b09df138d4e62895
+      md5sum: 0bc949aaa8792cd6c537cdaab0e2c145
 
 - name: gatk4 markduplicates test_gatk4_markduplicates_multiple_bams
   command: nextflow run tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_bams -c tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicates/nextflow.config
@@ -19,9 +19,9 @@
     - gatk4/markduplicates
   files:
     - path: output/gatk4/test.bai
-      md5sum: 325932c51f6898b02dfec469c984ba28
+      md5sum: bad71df9c876e72a5bc0a3e0fd755f92
     - path: output/gatk4/test.bam
-      md5sum: f7cba8104e3a7024a5e00c02304f7dea
+      md5sum: 8187febc6108ffef7f907e89b9c091a4
     - path: output/gatk4/test.metrics
     - path: output/gatk4/versions.yml
-      md5sum: 14d0d085df7d2f9e770578d92c329299
+      md5sum: b10d63cf7b2b672915cb30cea081ccd5

tests/modules/gatk4/splitncigarreads/test.yml

@@ -5,6 +5,6 @@
     - gatk4/splitncigarreads
   files:
     - path: output/gatk4/test.bam
-      md5sum: 1d54057d9f403fba2068ac1aaa4b8a28
+      md5sum: ceed15c0bd64ff5c38d3816905933b0b
     - path: output/gatk4/versions.yml
-      md5sum: f0f29af552075dc6bf8a13028e09f8e4
+      md5sum: 27fceace2528a905ddca2b4db47c4bf5

tests/modules/gatk4/variantrecalibrator/main.nf

@@ -2,7 +2,8 @@
 
 nextflow.enable.dsl = 2
 
-include { GATK4_VARIANTRECALIBRATOR } from '../../../../modules/gatk4/variantrecalibrator/main.nf'
+include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_NO_ALLELESPECIFICTY } from '../../../../modules/gatk4/variantrecalibrator/main.nf'
+include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY } from '../../../../modules/gatk4/variantrecalibrator/main.nf'
 
 workflow test_gatk4_variantrecalibrator {
 
@@ -14,7 +15,6 @@ workflow test_gatk4_variantrecalibrator {
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
     fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
     dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-    allelespecific = false
     resources = [
                  [
                  file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true),
@@ -35,11 +35,8 @@ workflow test_gatk4_variantrecalibrator {
                  'dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz'
                  ]
                 ]
-    annotation = ['QD', 'MQ', 'FS', 'SOR']
-    mode = 'SNP'
-    create_rscript = false
 
-    GATK4_VARIANTRECALIBRATOR ( input, fasta, fai, dict, allelespecific, resources, annotation, mode, create_rscript)
+    GATK4_VARIANTRECALIBRATOR_NO_ALLELESPECIFICTY ( input, fasta, fai, dict, resources)
 }
 
 workflow test_gatk4_variantrecalibrator_allele_specific {
@@ -52,7 +49,6 @@ workflow test_gatk4_variantrecalibrator_allele_specific {
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
     fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
     dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-    allelespecific = true
     resources = [
                  [
                  file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true),
@@ -73,9 +69,6 @@ workflow test_gatk4_variantrecalibrator_allele_specific {
                  'dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz'
                  ]
                 ]
-    annotation = ['QD', 'MQ', 'FS']
-    mode = 'SNP'
-    create_rscript = false
 
-    GATK4_VARIANTRECALIBRATOR ( input, fasta, fai, dict, allelespecific, resources, annotation, mode, create_rscript)
+    GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY ( input, fasta, fai, dict, resources)
 }

tests/modules/gatk4/variantrecalibrator/nextflow.config

@@ -1,5 +1,11 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
+    withName: GATK4_VARIANTRECALIBRATOR {
+        ext.args = '--mode SNP -an QD -an MQ -an FS -an SOR'
+    }
+
+    withName: GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY {
+        ext.args = '--mode SNP -an QD -an MQ -an FS -AS'
+    }
 }