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Merge pull request #1743 from FriederikeHanssen/update_spark

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gatk4 version update to 4.2.6.1
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FriederikeHanssen 2022-06-09 16:06:44 +02:00 committed by GitHub
commit a427bd587f
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4 changed files with 6 additions and 13 deletions
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6
modules/gatk4/applybqsrspark/main.nf
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@ -2,10 +2,8 @@ process GATK4_APPLYBQSR_SPARK {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1 conda-forge::openjdk=8.0.312" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container 'broadinstitute/gatk:4.2.6.1'
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)

6
modules/gatk4/baserecalibratorspark/main.nf
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@ -2,10 +2,8 @@ process GATK4_BASERECALIBRATOR_SPARK {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1 conda-forge::openjdk=8.0.312" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container 'broadinstitute/gatk:4.2.6.1'
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(input), path(input_index), path(intervals) tuple val(meta), path(input), path(input_index), path(intervals)

6
modules/gatk4/markduplicatesspark/main.nf
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@ -2,10 +2,8 @@ process GATK4_MARKDUPLICATES_SPARK {
tag "$meta.id" tag "$meta.id"
label 'process_high' label 'process_high'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0 conda-forge::openjdk=8.0.312" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1 conda-forge::openjdk=8.0.312" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container 'broadinstitute/gatk:4.2.6.1'
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'broadinstitute/gatk:4.2.3.0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

1
tests/modules/gatk4/applybqsrspark/test.yml
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@ -15,7 +15,6 @@
- gatk4/applybqsrspark - gatk4/applybqsrspark
files: files:
- path: output/gatk4/test.bam - path: output/gatk4/test.bam
md5sum: 2ca2446f0125890280056fd7da822732
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
- name: gatk4 applybqsr test_gatk4_applybqsr_spark_cram - name: gatk4 applybqsr test_gatk4_applybqsr_spark_cram