Merge branch 'master' into antismashlite

modules/gatk4/applybqsr/main.nf

@@ -2,10 +2,10 @@ process GATK4_APPLYBQSR {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)

modules/gatk4/applybqsrspark/main.nf

@@ -2,10 +2,10 @@ process GATK4_APPLYBQSR_SPARK {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)

modules/gatk4/applyvqsr/main.nf

@@ -2,10 +2,10 @@ process GATK4_APPLYVQSR {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches)

modules/gatk4/baserecalibrator/main.nf

@@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals)

modules/gatk4/baserecalibratorspark/main.nf

@@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR_SPARK {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'broadinstitute/gatk:4.2.3.0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--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=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--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=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(pileup), path(matched)

modules/gatk4/combinegvcfs/main.nf

@@ -2,10 +2,10 @@ process GATK4_COMBINEGVCFS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(vcf_idx)

modules/gatk4/createsequencedictionary/main.nf

@@ -2,10 +2,10 @@ process GATK4_CREATESEQUENCEDICTIONARY {
     tag "$fasta"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--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=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--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=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input)

modules/gatk4/fastqtosam/main.nf

@@ -2,10 +2,10 @@ process GATK4_FASTQTOSAM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--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=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate)

modules/gatk4/gatherbqsrreports/main.nf

@@ -2,10 +2,10 @@ process GATK4_GATHERBQSRREPORTS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(table)

modules/gatk4/gatherpileupsummaries/main.nf

@@ -2,10 +2,10 @@ process GATK4_GATHERPILEUPSUMMARIES {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
 
     input:

modules/gatk4/genomicsdbimport/main.nf

@@ -2,10 +2,10 @@ process GATK4_GENOMICSDBIMPORT {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace)

modules/gatk4/genotypegvcfs/main.nf

@@ -2,10 +2,10 @@ process GATK4_GENOTYPEGVCFS {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index)

modules/gatk4/getpileupsummaries/main.nf

@@ -2,10 +2,10 @@ process GATK4_GETPILEUPSUMMARIES {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(index), path(intervals)
@@ -40,7 +40,7 @@ process GATK4_GETPILEUPSUMMARIES {
         --variant $variants \\
         --output ${prefix}.pileups.table \\
         $reference_command \\
-        $sites_command \\
+        $interval_command \\
         --tmp-dir . \\
         $args
 

modules/gatk4/haplotypecaller/main.nf

@@ -2,10 +2,10 @@ process GATK4_HAPLOTYPECALLER {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--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=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(feature_file)

modules/gatk4/intervallisttobed/main.nf

@@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOBED {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(intervals)

modules/gatk4/intervallisttools/main.nf

@@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOOLS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(intervals)

modules/gatk4/learnreadorientationmodel/main.nf

@@ -2,10 +2,10 @@ process GATK4_LEARNREADORIENTATIONMODEL {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--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=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/gatk4/mergebamalignment/main.nf

@@ -2,10 +2,10 @@ process GATK4_MERGEBAMALIGNMENT {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(aligned), path(unmapped)

modules/gatk4/mergemutectstats/main.nf

@@ -2,10 +2,10 @@ process GATK4_MERGEMUTECTSTATS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(stats)

modules/gatk4/mergevcfs/main.nf

@@ -2,10 +2,10 @@ process GATK4_MERGEVCFS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf)

modules/gatk4/mutect2/main.nf

@@ -2,10 +2,10 @@ process GATK4_MUTECT2 {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals)

modules/gatk4/revertsam/main.nf

@@ -2,10 +2,10 @@ process GATK4_REVERTSAM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--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=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/gatk4/selectvariants/main.nf

@@ -2,10 +2,10 @@ process GATK4_SELECTVARIANTS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0':
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(vcf_idx)

modules/gatk4/splitncigarreads/main.nf

@@ -2,10 +2,10 @@ process GATK4_SPLITNCIGARREADS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai), path(intervals)

modules/gatk4/variantfiltration/main.nf

@@ -2,10 +2,10 @@ process GATK4_VARIANTFILTRATION {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)

modules/gatk4/variantrecalibrator/main.nf

@@ -2,10 +2,10 @@ process GATK4_VARIANTRECALIBRATOR {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)

tests/modules/gatk4/applybqsr/test.yml

@@ -5,7 +5,7 @@
     - gatk4/applybqsr
   files:
     - path: output/gatk4/test.bam
-      md5sum: d088422be886dc8507ff97fcc7dd968a
+      md5sum: e11b7eaf2034740a953626518e3c3d6e
     - path: output/gatk4/versions.yml
 
 - name: gatk4 applybqsr test_gatk4_applybqsr_intervals
@@ -15,7 +15,7 @@
     - gatk4/applybqsr
   files:
     - path: output/gatk4/test.bam
-      md5sum: 4bfa18d651abd945e240b05e70107716
+      md5sum: e9e9aa753c106e43f936ad573e23d2e6
     - path: output/gatk4/versions.yml
 
 - name: gatk4 applybqsr test_gatk4_applybqsr_cram
@@ -25,5 +25,5 @@
     - gatk4/applybqsr
   files:
     - path: output/gatk4/test.cram
-      md5sum: 2e0bca197af4f043a4a85152e6edbe04
+      md5sum: bca9d234a5d484ce2a6f4826ca2ea308
     - path: output/gatk4/versions.yml

tests/modules/gatk4/applybqsrspark/test.yml

@@ -5,7 +5,7 @@
     - gatk4/applybqsrspark
   files:
     - path: output/gatk4/test.bam
-      md5sum: d088422be886dc8507ff97fcc7dd968a
+      md5sum: 1901c819fcba0fdd5e2482e6dc8285ef
     - path: output/gatk4/versions.yml
 
 - name: gatk4 applybqsr test_gatk4_applybqsr_spark_intervals
@@ -15,7 +15,7 @@
     - gatk4/applybqsrspark
   files:
     - path: output/gatk4/test.bam
-      md5sum: 4bfa18d651abd945e240b05e70107716
+      md5sum: 2ca2446f0125890280056fd7da822732
     - path: output/gatk4/versions.yml
 
 - name: gatk4 applybqsr test_gatk4_applybqsr_spark_cram
@@ -25,5 +25,5 @@
     - gatk4/applybqsrspark
   files:
     - path: output/gatk4/test.cram
-      md5sum: 2e0bca197af4f043a4a85152e6edbe04
+      md5sum: 60f7c822a9f2833e11eb7bfd16e4421f
     - path: output/gatk4/versions.yml

tests/modules/gatk4/combinegvcfs/nextflow.config

@@ -1,6 +1,5 @@
 process {
 
-    ext.args = "--tmp-dir ."
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
 }

tests/modules/gatk4/genotypegvcfs/main.nf

@@ -65,7 +65,9 @@ workflow test_gatk4_genotypegvcfs_gz_input_intervals {
     input = [ [ id:'test' ], // meta map
             file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
             file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ]
+            file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ,
+            []
+            ]
 
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
@@ -80,7 +82,8 @@ workflow test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals {
     input = [ [ id:'test' ], // meta map
             file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
             file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+            file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
+            []
         ]
 
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
@@ -106,6 +109,7 @@ workflow test_gatk4_genotypegvcfs_gendb_input {
     gendb = UNTAR.out.untar.map{ it[1] }.collect()
     gendb.add([])
     gendb.add([])
+    gendb.add([])
 
     input = Channel.of([ id:'test' ]).combine(gendb)
 
@@ -128,6 +132,7 @@ workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp {
     gendb = UNTAR.out.untar.map{ it[1] }.collect()
     gendb.add([])
     gendb.add([])
+    gendb.add([])
     input = Channel.of([ id:'test' ]).combine(gendb)
 
     GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi)
@@ -146,6 +151,8 @@ workflow test_gatk4_genotypegvcfs_gendb_input_intervals {
     gendb = UNTAR.out.untar.map{ it[1] }.collect()
     gendb.add([])
     gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
+    gendb.add([])
+
     input = Channel.of([ id:'test' ]).combine(gendb)
 
     GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [] )
@@ -167,6 +174,8 @@ workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals {
     gendb = UNTAR.out.untar.map{ it[1] }.collect()
     gendb.add([])
     gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
+    gendb.add([])
+
     input = Channel.of([ id:'test' ]).combine(gendb)
 
     GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi )

tests/modules/gatk4/getpileupsummaries/main.nf

@@ -4,21 +4,6 @@ nextflow.enable.dsl = 2
 
 include { GATK4_GETPILEUPSUMMARIES } from '../../../../modules/gatk4/getpileupsummaries/main.nf'
 
-workflow test_gatk4_getpileupsummaries_just_variants {
-
-    input = [ [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true) ,
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
-        []
-        ]
-
-    variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
-    variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
-    fasta = []
-    fai = []
-    dict = []
-    GATK4_GETPILEUPSUMMARIES ( input , fasta, fai, dict, variants , variants_tbi )
-}
 
 workflow test_gatk4_getpileupsummaries_separate_sites {
 

tests/modules/gatk4/getpileupsummaries/test.yml

@@ -1,13 +1,3 @@
-- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_just_variants
-  command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_just_variants -c tests/config/nextflow.config
-  tags:
-    - gatk4/getpileupsummaries
-    - gatk4
-  files:
-    - path: output/gatk4/test.pileups.table
-      md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
-    - path: output/gatk4/versions.yml
-
 - 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
   tags:

tests/modules/gatk4/intervallisttools/test.yml

@@ -7,11 +7,11 @@
     - path: output/gatk4/test.interval_list
       md5sum: e51101c9357fb2d59fd30e370eefa39c
     - path: output/gatk4/test_split/temp_0001_of_6/1scattered.interval_list
-      md5sum: b8ba8a387200df76a0d1c577626dc265
+      md5sum: 39385d38ac6cb7c05190026fc3b81411
     - path: output/gatk4/test_split/temp_0002_of_6/2scattered.interval_list
-      md5sum: 0728d164666d9264ef442a493e008dee
+      md5sum: 59f1978c5f4ef3fce3b110816283d9f5
     - path: output/gatk4/test_split/temp_0003_of_6/3scattered.interval_list
-      md5sum: 55da0f3c69504148f4e7002a0e072cfe
+      md5sum: 709fe81bfcf700bd80d96c62a71629fd
     - path: output/gatk4/test_split/temp_0004_of_6/4scattered.interval_list
-      md5sum: d29ca4447f32547f2936567fa902796a
+      md5sum: c24044490cfedbcba61dbc646d3aa570
     - path: output/gatk4/versions.yml

tests/modules/gatk4/markduplicates/test.yml

@@ -5,9 +5,9 @@
     - gatk4/markduplicates
   files:
     - path: output/gatk4/test.bai
-      md5sum: e9c125e82553209933883b4fe2b8d7c2
+      md5sum: c8f7a9e426c768577f88f59cb1336bf3
     - path: output/gatk4/test.bam
-      md5sum: 2efd50b2e6b7fd9bdf242cd9e266cfa9
+      md5sum: 58533ddab47f7ac07f7b10e7f4aac234
     - path: output/gatk4/test.metrics
     - path: output/gatk4/versions.yml
 
@@ -20,6 +20,6 @@
     - path: output/gatk4/test.bai
       md5sum: bad71df9c876e72a5bc0a3e0fd755f92
     - path: output/gatk4/test.bam
-      md5sum: 8187febc6108ffef7f907e89b9c091a4
+      md5sum: 112580c24b43331950f24f9adea30788
     - path: output/gatk4/test.metrics
     - path: output/gatk4/versions.yml

tests/modules/gatk4/splitncigarreads/test.yml

@@ -5,7 +5,7 @@
     - gatk4/splitncigarreads
   files:
     - path: output/gatk4/test.bam
-      md5sum: 436d8e31285c6b588bdd1c7f1d07f6f2
+      md5sum: 37e5dbce8692b54c3292b539c91dfbd7
     - path: output/gatk4/versions.yml
 - name: gatk4 splitncigarreads test_gatk4_splitncigarreads_intervals
   command: nextflow run tests/modules/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads_intervals -c tests/config/nextflow.config
@@ -14,5 +14,5 @@
     - gatk4/splitncigarreads
   files:
     - path: output/gatk4/test.bam
-      md5sum: cd56e3225950f519fd47164cca60a0bb
+      md5sum: e5cd2fd1822298a9bf7bc8b8d42146af
     - path: output/gatk4/versions.yml

tests/modules/gatk4/variantrecalibrator/test.yml

@@ -9,7 +9,7 @@
         - "#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO"
     - path: output/gatk4/test.recal.idx
     - path: output/gatk4/test.tranches
-      md5sum: d238e97bf996863969dac7751e345549
+      md5sum: c029e52fd63a893e1154cc9144a19eeb
     - path: output/gatk4/versions.yml
 
 - name: gatk4 variantrecalibrator test_gatk4_variantrecalibrator_allele_specific
@@ -23,5 +23,5 @@
         - "#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO"
     - path: output/gatk4/test.recal.idx
     - path: output/gatk4/test.tranches
-      md5sum: 444438d46716593634a6817958099292
+      md5sum: ad52fa69325c758f458a30ee5b43d6b5
     - path: output/gatk4/versions.yml