Log4j again (#1202)

* Log4j again * Update checksums
2024-12-22 02:58:17 +00:00 · 2022-01-12 13:55:54 +01:00 · 2022-01-12 13:55:54 +01:00 · 598d7abdb2
commit 598d7abdb2
parent 05ba4d901d
36 changed files with 111 additions and 111 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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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
@ -2,10 +2,10 @@ process GATK4_APPLYVQSR {
    tag "$meta.id"
    label 'process_low'

-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"

    input:
    tuple val(meta), path(vcf), path(tbi), path(recal), path(recalidx), path(tranches)
--- 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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"

    input:
    tuple val(meta), path(bam), path(bai)
--- 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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"

    input:
    tuple val(meta), path(aligned)
--- 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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"

    input:
    tuple val(meta) , path(input) , path(input_index) , 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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--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=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"

    input:
    tuple val(meta), path(vcf), path(vcf_tbi)
--- a/modules/gatk4/variantrecalibrator/main.nf
+++ b/modules/gatk4/variantrecalibrator/main.nf
@ -2,10 +2,10 @@ process GATK4_VARIANTRECALIBRATOR {
    tag "$meta.id"
    label 'process_low'

-        conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
-        container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-            'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
-            'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    container "${ 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' }"

    input:
    tuple val(meta), path(vcf) , path(tbi)
--- 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: 8fe7c4b5fcfb72d24ed8102eb26e42fb
+      md5sum: 908825edf1f229a072f91d8b753d95dd
    - path: output/gatk4/versions.yml
-      md5sum: 8a2fb7c7e38f24d3fefd5e84da701b00
+      md5sum: b65c46529ae9658db0c596cbc26505c2

 - 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: a7a1d1373ac1529abbc5e05359718ab1
+      md5sum: 50f8a79c7d528e02470416f81eb582bc
    - path: output/gatk4/versions.yml
-      md5sum: 550eecbb88887fadf8c62c5992ae48af
+      md5sum: 17c8a40b3537e3400edebd1826d28385

 - 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: b7659b3b2adaabbe73658dc059dbfdf6
+      md5sum: cd8d4ba6181f714e74641adeb2f9aa1d
    - path: output/gatk4/versions.yml
-      md5sum: 57933f27b3a31b05af3f7c248d365396
+      md5sum: 35218922e1929c699ea64de9f4c29fb5
--- 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: 984c932ee9a5683b18e22a369aa5c9e7
+      md5sum: 524a78cdfa56c8b09a4ff3f4cb278261

 - 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: 3b55f26c94c5f145f10ef4c5f83ec3cc
+      md5sum: 7a3c6e97628bd1f5f4e7fd429bf74a8e
--- 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: 6f2396e71389cdfd184f91222c24fe8d
+      md5sum: 79575dc2e6a7f0361f2d8b090c496070

 - 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: 26863fa1e7e7d50d1a10761eced26062
+      md5sum: 733f15ef7eb504daec9fd8cd9beef71a

 - 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: 8b1191953ff20660e06e2a5d79e96b02
+      md5sum: 5396e33146addbe4a59d0f30cb573a3a
--- 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: db3fa4b463427b08e32a5d8264be59c1
+      md5sum: 03f3accdc3e3c392c1179213286a0b67

 - 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: f4e35e46a29d8faebda5e852f9d0a132
+      md5sum: 144e7118d5f277ad5fba863213c810b0
--- 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: 2fa1214574359aa7c4e2212efbae3714
+      md5sum: b53101f71b0763e80855703ba4e1f101

 - 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: 92c17a728cef6d458491bcec6dac3e0c
+      md5sum: 584a6ebf04f54abcfcf4c8255e13ff2a
--- 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: 92e9e7db68d22df72adc02e59fab1eb7
+      md5sum: 6fffaf981f099659cf820277d1f3c606

 - 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: b3fcd07c2f498a2ad503912524d74294
+      md5sum: 4a56022d6e08d54e8ba853637bf3b5f1
    - 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: f204d259538a490b40c1fe787a3d6602
+      md5sum: da6a815b7340683b1a56bdfd7e66d463
    - path: output/untar/versions.yml
      md5sum: 9b2916aea9790bdf427c0cb38109110c
--- 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: e574bd51e4c6d6ded5dcf3cd865dbf4a
+      md5sum: 9eb24dc17c96971b7991b3e154279aa7

 - 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: fee70d33f4379ced035d8e851a3e08c6
+      md5sum: f76543e715342bf1fcdeb20385e01fe9

 - 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: 29bddb019f0fe04218cfc07f8203e022
+      md5sum: a5d988cf62648f700ffac7257e72b2c0
--- 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: e9c125e82553209933883b4fe2b8d7c2
+      md5sum: c8f7a9e426c768577f88f59cb1336bf3
    - path: output/gatk4/test.bam
-      md5sum: 1c6b1372121eddccd086456aa1c174bf
+      md5sum: fba0c99a0b087c90113a210e4465f91b
    - path: output/gatk4/test.metrics
    - path: output/gatk4/versions.yml
-      md5sum: 0e46677bdf1e5df892578cec6bc26dba
+      md5sum: dacbab0e112d2403b09df138d4e62895

 - 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: bad71df9c876e72a5bc0a3e0fd755f92
+      md5sum: 325932c51f6898b02dfec469c984ba28
    - path: output/gatk4/test.bam
-      md5sum: d1b85fb578a97f05b484c0d241a9aaad
+      md5sum: f7cba8104e3a7024a5e00c02304f7dea
    - path: output/gatk4/test.metrics
    - path: output/gatk4/versions.yml
-      md5sum: 6844dc08e677455205e2270ac291c951
+      md5sum: 14d0d085df7d2f9e770578d92c329299
--- 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: 03068d510523c996814256d9811dc272
+      md5sum: 1d54057d9f403fba2068ac1aaa4b8a28
    - path: output/gatk4/versions.yml
-      md5sum: de130e0ab817304404f296b2e512b3b8
+      md5sum: f0f29af552075dc6bf8a13028e09f8e4