From 169b2b96c1167f89ab07127b7057c1d90a6996c7 Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Thu, 12 May 2022 15:45:21 +0200
Subject: [PATCH 01/14] update gatk version

---
 modules/gatk4/applybqsr/main.nf                   | 6 +++---
 modules/gatk4/applybqsrspark/main.nf              | 6 +++---
 modules/gatk4/applyvqsr/main.nf                   | 6 +++---
 modules/gatk4/baserecalibrator/main.nf            | 6 +++---
 modules/gatk4/bedtointervallist/main.nf           | 6 +++---
 modules/gatk4/calculatecontamination/main.nf      | 6 +++---
 modules/gatk4/combinegvcfs/main.nf                | 6 +++---
 modules/gatk4/createsequencedictionary/main.nf    | 6 +++---
 modules/gatk4/createsomaticpanelofnormals/main.nf | 6 +++---
 modules/gatk4/estimatelibrarycomplexity/main.nf   | 6 +++---
 modules/gatk4/fastqtosam/main.nf                  | 6 +++---
 modules/gatk4/filtermutectcalls/main.nf           | 6 +++---
 modules/gatk4/gatherbqsrreports/main.nf           | 6 +++---
 modules/gatk4/gatherpileupsummaries/main.nf       | 6 +++---
 modules/gatk4/genomicsdbimport/main.nf            | 6 +++---
 modules/gatk4/genotypegvcfs/main.nf               | 6 +++---
 modules/gatk4/getpileupsummaries/main.nf          | 6 +++---
 modules/gatk4/haplotypecaller/main.nf             | 6 +++---
 modules/gatk4/indexfeaturefile/main.nf            | 6 +++---
 modules/gatk4/intervallisttobed/main.nf           | 6 +++---
 modules/gatk4/intervallisttools/main.nf           | 6 +++---
 modules/gatk4/learnreadorientationmodel/main.nf   | 6 +++---
 modules/gatk4/markduplicates/main.nf              | 6 +++---
 modules/gatk4/mergebamalignment/main.nf           | 6 +++---
 modules/gatk4/mergemutectstats/main.nf            | 6 +++---
 modules/gatk4/mergevcfs/main.nf                   | 6 +++---
 modules/gatk4/mutect2/main.nf                     | 6 +++---
 modules/gatk4/revertsam/main.nf                   | 6 +++---
 modules/gatk4/samtofastq/main.nf                  | 6 +++---
 modules/gatk4/selectvariants/main.nf              | 6 +++---
 modules/gatk4/splitncigarreads/main.nf            | 6 +++---
 modules/gatk4/variantfiltration/main.nf           | 6 +++---
 modules/gatk4/variantrecalibrator/main.nf         | 6 +++---
 33 files changed, 99 insertions(+), 99 deletions(-)

diff --git a/modules/gatk4/applybqsr/main.nf b/modules/gatk4/applybqsr/main.nf
index 7a64dab2..a0e2c45c 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
diff --git a/modules/gatk4/applybqsrspark/main.nf b/modules/gatk4/applybqsrspark/main.nf
index 04303c09..9d7891ba 100644
--- a/modules/gatk4/applybqsrspark/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
diff --git a/modules/gatk4/applyvqsr/main.nf b/modules/gatk4/applyvqsr/main.nf
index 8b235809..d3da8332 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches)
diff --git a/modules/gatk4/baserecalibrator/main.nf b/modules/gatk4/baserecalibrator/main.nf
index 766a8338..fb26d3da 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals)
diff --git a/modules/gatk4/bedtointervallist/main.nf b/modules/gatk4/bedtointervallist/main.nf
index 118f535b..6224d9b3 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bed)
diff --git a/modules/gatk4/calculatecontamination/main.nf b/modules/gatk4/calculatecontamination/main.nf
index 197fe6c2..c289684e 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(pileup), path(matched)
diff --git a/modules/gatk4/combinegvcfs/main.nf b/modules/gatk4/combinegvcfs/main.nf
index 45bf4372..db4d9cdb 100644
--- a/modules/gatk4/combinegvcfs/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(vcf_idx)
diff --git a/modules/gatk4/createsequencedictionary/main.nf b/modules/gatk4/createsequencedictionary/main.nf
index dbf37048..13fa9e81 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     path fasta
diff --git a/modules/gatk4/createsomaticpanelofnormals/main.nf b/modules/gatk4/createsomaticpanelofnormals/main.nf
index 3df29947..653a9497 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(genomicsdb)
diff --git a/modules/gatk4/estimatelibrarycomplexity/main.nf b/modules/gatk4/estimatelibrarycomplexity/main.nf
index caa34630..46e09a95 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input)
diff --git a/modules/gatk4/fastqtosam/main.nf b/modules/gatk4/fastqtosam/main.nf
index 199058d0..326d4d58 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/gatk4/filtermutectcalls/main.nf b/modules/gatk4/filtermutectcalls/main.nf
index c1c82e0b..91f6defa 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate)
diff --git a/modules/gatk4/gatherbqsrreports/main.nf b/modules/gatk4/gatherbqsrreports/main.nf
index 1f5f2e1b..231bd39e 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(table)
diff --git a/modules/gatk4/gatherpileupsummaries/main.nf b/modules/gatk4/gatherpileupsummaries/main.nf
index f5e9cf22..0b763f41 100644
--- a/modules/gatk4/gatherpileupsummaries/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
 
     input:
diff --git a/modules/gatk4/genomicsdbimport/main.nf b/modules/gatk4/genomicsdbimport/main.nf
index d2b78899..810f2b63 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace)
diff --git a/modules/gatk4/genotypegvcfs/main.nf b/modules/gatk4/genotypegvcfs/main.nf
index 0df88d66..11024b1b 100644
--- a/modules/gatk4/genotypegvcfs/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index)
diff --git a/modules/gatk4/getpileupsummaries/main.nf b/modules/gatk4/getpileupsummaries/main.nf
index c0946f71..67e9276c 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(index), path(intervals)
diff --git a/modules/gatk4/haplotypecaller/main.nf b/modules/gatk4/haplotypecaller/main.nf
index 2cd9e7d4..6dd3f69e 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals)
diff --git a/modules/gatk4/indexfeaturefile/main.nf b/modules/gatk4/indexfeaturefile/main.nf
index 90ff94e6..264f71ef 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(feature_file)
diff --git a/modules/gatk4/intervallisttobed/main.nf b/modules/gatk4/intervallisttobed/main.nf
index c0f9df63..84f3c472 100644
--- a/modules/gatk4/intervallisttobed/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(intervals)
diff --git a/modules/gatk4/intervallisttools/main.nf b/modules/gatk4/intervallisttools/main.nf
index 1b9b37f4..7ab26c15 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(intervals)
diff --git a/modules/gatk4/learnreadorientationmodel/main.nf b/modules/gatk4/learnreadorientationmodel/main.nf
index 717cf211..8c4ac94e 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(f1r2)
diff --git a/modules/gatk4/markduplicates/main.nf b/modules/gatk4/markduplicates/main.nf
index 2650925b..97a8c3e1 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/gatk4/mergebamalignment/main.nf b/modules/gatk4/mergebamalignment/main.nf
index 5c36b4ba..ff51de06 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(aligned), path(unmapped)
diff --git a/modules/gatk4/mergemutectstats/main.nf b/modules/gatk4/mergemutectstats/main.nf
index 409e06f6..54311df7 100644
--- a/modules/gatk4/mergemutectstats/main.nf
+++ b/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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(stats)
diff --git a/modules/gatk4/mergevcfs/main.nf b/modules/gatk4/mergevcfs/main.nf
index 06ff3acb..964c1a3b 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf)
diff --git a/modules/gatk4/mutect2/main.nf b/modules/gatk4/mutect2/main.nf
index 9969ad70..abec0d73 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals)
diff --git a/modules/gatk4/revertsam/main.nf b/modules/gatk4/revertsam/main.nf
index 3084658d..959c3e79 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/gatk4/samtofastq/main.nf b/modules/gatk4/samtofastq/main.nf
index d8d94d69..de83293a 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/gatk4/selectvariants/main.nf b/modules/gatk4/selectvariants/main.nf
index 22779211..633c21f2 100644
--- a/modules/gatk4/selectvariants/main.nf
+++ b/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':
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(vcf_idx)
diff --git a/modules/gatk4/splitncigarreads/main.nf b/modules/gatk4/splitncigarreads/main.nf
index 85e5daa8..456ec055 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai), path(intervals)
diff --git a/modules/gatk4/variantfiltration/main.nf b/modules/gatk4/variantfiltration/main.nf
index 6beb87ef..cda06e11 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)
diff --git a/modules/gatk4/variantrecalibrator/main.nf b/modules/gatk4/variantrecalibrator/main.nf
index cdcc1221..120aeade 100644
--- 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=4.2.5.0" : 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' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)

From fd7ee6799abf1bd5228b4b59ce541f3aeaa2280b Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Thu, 12 May 2022 15:55:11 +0200
Subject: [PATCH 02/14] update version also for spark containers

---
 modules/gatk4/baserecalibratorspark/main.nf | 6 +++---
 modules/gatk4/markduplicatesspark/main.nf   | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/gatk4/baserecalibratorspark/main.nf b/modules/gatk4/baserecalibratorspark/main.nf
index 70c70181..79988b72 100644
--- a/modules/gatk4/baserecalibratorspark/main.nf
+++ b/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' :
-        'broadinstitute/gatk:4.2.3.0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals)
diff --git a/modules/gatk4/markduplicatesspark/main.nf b/modules/gatk4/markduplicatesspark/main.nf
index 77e135db..e3872c6e 100644
--- a/modules/gatk4/markduplicatesspark/main.nf
+++ b/modules/gatk4/markduplicatesspark/main.nf
@@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES_SPARK {
     tag "$meta.id"
     label 'process_high'
 
-    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' :
-        'broadinstitute/gatk:4.2.3.0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

From fef5434c4cfdc8a7637b9b430298963574290128 Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Thu, 12 May 2022 16:07:12 +0200
Subject: [PATCH 03/14] Update md5sums

---
 tests/modules/gatk4/applybqsr/test.yml           | 6 +++---
 tests/modules/gatk4/applybqsrspark/test.yml      | 6 +++---
 tests/modules/gatk4/intervallisttools/test.yml   | 8 ++++----
 tests/modules/gatk4/markduplicates/test.yml      | 6 +++---
 tests/modules/gatk4/splitncigarreads/test.yml    | 4 ++--
 tests/modules/gatk4/variantrecalibrator/test.yml | 4 ++--
 6 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/tests/modules/gatk4/applybqsr/test.yml b/tests/modules/gatk4/applybqsr/test.yml
index eaf1a08e..c3dd4eef 100644
--- a/tests/modules/gatk4/applybqsr/test.yml
+++ b/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
diff --git a/tests/modules/gatk4/applybqsrspark/test.yml b/tests/modules/gatk4/applybqsrspark/test.yml
index d230c000..1e4f8b47 100644
--- a/tests/modules/gatk4/applybqsrspark/test.yml
+++ b/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
diff --git a/tests/modules/gatk4/intervallisttools/test.yml b/tests/modules/gatk4/intervallisttools/test.yml
index 5542714b..89367a09 100644
--- a/tests/modules/gatk4/intervallisttools/test.yml
+++ b/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
diff --git a/tests/modules/gatk4/markduplicates/test.yml b/tests/modules/gatk4/markduplicates/test.yml
index 1fbd768e..d3a9f269 100644
--- a/tests/modules/gatk4/markduplicates/test.yml
+++ b/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
diff --git a/tests/modules/gatk4/splitncigarreads/test.yml b/tests/modules/gatk4/splitncigarreads/test.yml
index d9a58901..261f7bc3 100644
--- a/tests/modules/gatk4/splitncigarreads/test.yml
+++ b/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
diff --git a/tests/modules/gatk4/variantrecalibrator/test.yml b/tests/modules/gatk4/variantrecalibrator/test.yml
index bc84bfb3..39931137 100644
--- a/tests/modules/gatk4/variantrecalibrator/test.yml
+++ b/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

From 15fbf21b28a13cfaa043cfbdc12a9538c87ff4f4 Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Thu, 12 May 2022 16:16:53 +0200
Subject: [PATCH 04/14] double tmpdir args removed, porb leftover after massive
 refactor where we decided to make it mandatory everywhere

---
 tests/modules/gatk4/combinegvcfs/nextflow.config | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/tests/modules/gatk4/combinegvcfs/nextflow.config b/tests/modules/gatk4/combinegvcfs/nextflow.config
index 573cc13e..8730f1c4 100644
--- a/tests/modules/gatk4/combinegvcfs/nextflow.config
+++ b/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()}" }
-    
-}
\ No newline at end of file
+
+}

From f40cfefc0899fd6bb6adc300142ca6c3a35573ff Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Thu, 12 May 2022 16:47:17 +0200
Subject: [PATCH 05/14] leftover fixes from refactoring

---
 modules/gatk4/getpileupsummaries/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/gatk4/getpileupsummaries/main.nf b/modules/gatk4/getpileupsummaries/main.nf
index 67e9276c..1c056170 100644
--- a/modules/gatk4/getpileupsummaries/main.nf
+++ b/modules/gatk4/getpileupsummaries/main.nf
@@ -40,7 +40,7 @@ process GATK4_GETPILEUPSUMMARIES {
         --variant $variants \\
         --output ${prefix}.pileups.table \\
         $reference_command \\
-        $sites_command \\
+        $interval_command \\
         --tmp-dir . \\
         $args
 

From b3bd55da7635eee872e748676614464067c33f75 Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Thu, 12 May 2022 16:51:17 +0200
Subject: [PATCH 06/14] getpileupsummaries requires intervals files

---
 tests/modules/gatk4/getpileupsummaries/main.nf  | 15 ---------------
 tests/modules/gatk4/getpileupsummaries/test.yml | 10 ----------
 2 files changed, 25 deletions(-)

diff --git a/tests/modules/gatk4/getpileupsummaries/main.nf b/tests/modules/gatk4/getpileupsummaries/main.nf
index b0de9d6e..2a53e35e 100644
--- a/tests/modules/gatk4/getpileupsummaries/main.nf
+++ b/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 {
 
diff --git a/tests/modules/gatk4/getpileupsummaries/test.yml b/tests/modules/gatk4/getpileupsummaries/test.yml
index 2e4acce9..2529fbc5 100644
--- a/tests/modules/gatk4/getpileupsummaries/test.yml
+++ b/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:

From a694267b4b138e4da4c98f17fcc4e4d0feff0056 Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Thu, 12 May 2022 17:01:03 +0200
Subject: [PATCH 07/14] fix empty index input

---
 tests/modules/gatk4/genotypegvcfs/main.nf | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tests/modules/gatk4/genotypegvcfs/main.nf b/tests/modules/gatk4/genotypegvcfs/main.nf
index 75990958..4caba697 100644
--- a/tests/modules/gatk4/genotypegvcfs/main.nf
+++ b/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)

From 8792d102ee9377ab6886033e3b821dc70df8e5ab Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Thu, 12 May 2022 17:37:06 +0200
Subject: [PATCH 08/14] fix test input

---
 tests/modules/gatk4/genotypegvcfs/main.nf | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/tests/modules/gatk4/genotypegvcfs/main.nf b/tests/modules/gatk4/genotypegvcfs/main.nf
index 4caba697..cd7d3a03 100644
--- a/tests/modules/gatk4/genotypegvcfs/main.nf
+++ b/tests/modules/gatk4/genotypegvcfs/main.nf
@@ -82,7 +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)
@@ -108,6 +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)
 
@@ -130,6 +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)
@@ -148,6 +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, [], [] )
@@ -169,6 +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 )

From 3fda3903dc255460fddbc730d7e5f103f7119df5 Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Thu, 12 May 2022 17:40:42 +0200
Subject: [PATCH 09/14] revert markduplciatespark container

---
 modules/gatk4/markduplicatesspark/main.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/gatk4/markduplicatesspark/main.nf b/modules/gatk4/markduplicatesspark/main.nf
index e3872c6e..77e135db 100644
--- a/modules/gatk4/markduplicatesspark/main.nf
+++ b/modules/gatk4/markduplicatesspark/main.nf
@@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES_SPARK {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
+    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/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
+        'broadinstitute/gatk:4.2.3.0' }"
 
     input:
     tuple val(meta), path(bam)

From 99880654bfab2ad611195a6e0d757eb1b2b12f88 Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Thu, 12 May 2022 18:06:15 +0200
Subject: [PATCH 10/14] add output default bam

---
 modules/gatk4/markduplicatesspark/main.nf               | 2 +-
 tests/modules/gatk4/markduplicatesspark/nextflow.config | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/modules/gatk4/markduplicatesspark/main.nf b/modules/gatk4/markduplicatesspark/main.nf
index 77e135db..a086cd7a 100644
--- a/modules/gatk4/markduplicatesspark/main.nf
+++ b/modules/gatk4/markduplicatesspark/main.nf
@@ -22,7 +22,7 @@ process GATK4_MARKDUPLICATES_SPARK {
 
     script:
     def args = task.ext.args ?: ''
-    prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}.bam"
     def input_list = bam.collect{"--input $it"}.join(' ')
 
     def avail_mem = 3
diff --git a/tests/modules/gatk4/markduplicatesspark/nextflow.config b/tests/modules/gatk4/markduplicatesspark/nextflow.config
index 8730f1c4..83411693 100644
--- a/tests/modules/gatk4/markduplicatesspark/nextflow.config
+++ b/tests/modules/gatk4/markduplicatesspark/nextflow.config
@@ -1,5 +1,4 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
 }

From e3a17b699e5b93a25ebd8ec4cc71ae4b7eb70285 Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Thu, 12 May 2022 18:19:33 +0200
Subject: [PATCH 11/14] update version

---
 modules/gatk4/markduplicatesspark/main.nf | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/modules/gatk4/markduplicatesspark/main.nf b/modules/gatk4/markduplicatesspark/main.nf
index a086cd7a..2ef91111 100644
--- a/modules/gatk4/markduplicatesspark/main.nf
+++ b/modules/gatk4/markduplicatesspark/main.nf
@@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES_SPARK {
     tag "$meta.id"
     label 'process_high'
 
-    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' :
-        'broadinstitute/gatk:4.2.3.0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -32,8 +32,6 @@ process GATK4_MARKDUPLICATES_SPARK {
         avail_mem = task.memory.giga
     }
     """
-    export SPARK_USER=spark3
-
     gatk --java-options "-Xmx${avail_mem}g" MarkDuplicatesSpark \\
         $input_list \\
         --output $prefix \\

From 5f7b02189ad35cb84fe595560894610986ea7f3d Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Thu, 12 May 2022 18:35:51 +0200
Subject: [PATCH 12/14] reverse again, why did tests pass before

---
 modules/gatk4/markduplicatesspark/main.nf | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/modules/gatk4/markduplicatesspark/main.nf b/modules/gatk4/markduplicatesspark/main.nf
index 2ef91111..4e01cccf 100644
--- a/modules/gatk4/markduplicatesspark/main.nf
+++ b/modules/gatk4/markduplicatesspark/main.nf
@@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES_SPARK {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
+    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/gatk4:4.2.6.1--hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
+        'broadinstitute/gatk:4.2.3.0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -22,7 +22,7 @@ process GATK4_MARKDUPLICATES_SPARK {
 
     script:
     def args = task.ext.args ?: ''
-    prefix = task.ext.prefix ?: "${meta.id}.bam"
+    prefix = task.ext.prefix ?: "${meta.id}"
     def input_list = bam.collect{"--input $it"}.join(' ')
 
     def avail_mem = 3
@@ -32,6 +32,10 @@ process GATK4_MARKDUPLICATES_SPARK {
         avail_mem = task.memory.giga
     }
     """
+    export SPARK_USER=spark3
+
+
+
     gatk --java-options "-Xmx${avail_mem}g" MarkDuplicatesSpark \\
         $input_list \\
         --output $prefix \\

From ba14355891706c985cc17e62427f419db1a3472c Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Mon, 16 May 2022 09:54:40 +0200
Subject: [PATCH 13/14] revert markduplciatespark changes

---
 modules/gatk4/markduplicatesspark/main.nf | 2 --
 1 file changed, 2 deletions(-)

diff --git a/modules/gatk4/markduplicatesspark/main.nf b/modules/gatk4/markduplicatesspark/main.nf
index 4e01cccf..77e135db 100644
--- a/modules/gatk4/markduplicatesspark/main.nf
+++ b/modules/gatk4/markduplicatesspark/main.nf
@@ -34,8 +34,6 @@ process GATK4_MARKDUPLICATES_SPARK {
     """
     export SPARK_USER=spark3
 
-
-
     gatk --java-options "-Xmx${avail_mem}g" MarkDuplicatesSpark \\
         $input_list \\
         --output $prefix \\

From eb841d4ea0b3a1d259b02d4b434921de5c32a019 Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Mon, 16 May 2022 10:33:01 +0200
Subject: [PATCH 14/14] revert markduplciatespark changes

---
 tests/modules/gatk4/markduplicatesspark/nextflow.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/modules/gatk4/markduplicatesspark/nextflow.config b/tests/modules/gatk4/markduplicatesspark/nextflow.config
index 83411693..8730f1c4 100644
--- a/tests/modules/gatk4/markduplicatesspark/nextflow.config
+++ b/tests/modules/gatk4/markduplicatesspark/nextflow.config
@@ -1,4 +1,5 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
 }