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
2024-11-10 20:23:10 +00:00 · 2022-02-15 11:29:36 +01:00 · 2022-02-15 11:29:36 +01:00 · 967fb22ded
commit 967fb22ded
parent 04e82ec61a
43 changed files with 136 additions and 189 deletions
--- a/modules/gatk4/applybqsr/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
--- a/modules/gatk4/applyvqsr/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--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
--- a/modules/gatk4/applyvqsr/meta.yml
+++ b/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:
--- a/modules/gatk4/baserecalibrator/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(input), path(input_index), path(intervals)
--- a/modules/gatk4/bedtointervallist/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(bed)
--- a/modules/gatk4/calculatecontamination/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(pileup), path(matched)
--- a/modules/gatk4/createsequencedictionary/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    path fasta
--- a/modules/gatk4/createsomaticpanelofnormals/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(genomicsdb)
--- a/modules/gatk4/estimatelibrarycomplexity/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(cram)
--- a/modules/gatk4/fastqtosam/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(reads)
--- a/modules/gatk4/filtermutectcalls/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(vcf), path(tbi), path(stats), path(orientationbias), path(segmentation), path(contaminationfile), val(contaminationest)
--- a/modules/gatk4/gatherbqsrreports/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(recal_table)
--- a/modules/gatk4/genomicsdbimport/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(vcf), path(tbi), path(intervalfile), val(intervalval), path(wspace)
--- a/modules/gatk4/genotypegvcfs/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(gvcf), path(gvcf_index), path(intervals)
--- a/modules/gatk4/getpileupsummaries/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(input), path(index), path(intervals)
--- a/modules/gatk4/haplotypecaller/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(input), path(input_index), path(intervals)
--- a/modules/gatk4/indexfeaturefile/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(feature_file)
--- a/modules/gatk4/intervallisttools/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(interval_list)
--- a/modules/gatk4/learnreadorientationmodel/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(f1r2)
--- a/modules/gatk4/markduplicates/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(bams)
--- a/modules/gatk4/mergebamalignment/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(aligned), path(unmapped)
--- a/modules/gatk4/mergevcfs/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(vcfs)
--- a/modules/gatk4/mutect2/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta) , path(input) , path(input_index) , path(intervals), val(which_norm)
--- a/modules/gatk4/revertsam/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(bam)
--- a/modules/gatk4/samtofastq/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(bam)
--- a/modules/gatk4/splitncigarreads/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(bam)
--- a/modules/gatk4/variantfiltration/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"

    input:
    tuple val(meta), path(vcf), path(vcf_tbi)
--- a/modules/gatk4/variantrecalibrator/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.5.0--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
--- a/modules/gatk4/variantrecalibrator/meta.yml
+++ b/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
--- a/tests/modules/gatk4/applybqsr/test.yml
+++ b/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
--- a/tests/modules/gatk4/applyvqsr/main.nf
+++ b/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)
 }
--- a/tests/modules/gatk4/applyvqsr/nextflow.config
+++ b/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'
+    }
 }
--- a/tests/modules/gatk4/applyvqsr/test.yml
+++ b/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
--- a/tests/modules/gatk4/calculatecontamination/test.yml
+++ b/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
--- a/tests/modules/gatk4/fastqtosam/test.yml
+++ b/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
--- a/tests/modules/gatk4/gatherbqsrreports/test.yml
+++ b/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
--- a/tests/modules/gatk4/genomicsdbimport/test.yml
+++ b/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
--- a/tests/modules/gatk4/getpileupsummaries/test.yml
+++ b/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
--- a/tests/modules/gatk4/indexfeaturefile/test.yml
+++ b/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
--- a/tests/modules/gatk4/markduplicates/test.yml
+++ b/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
--- a/tests/modules/gatk4/splitncigarreads/test.yml
+++ b/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
--- a/tests/modules/gatk4/variantrecalibrator/main.nf
+++ b/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)
 }
--- a/tests/modules/gatk4/variantrecalibrator/nextflow.config
+++ b/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'
+    }
 }