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reverse again, why did tests pass before

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Rike 2022-05-12 18:35:51 +02:00
parent e3a17b699e
commit 5f7b02189a
1 changed files with 8 additions and 4 deletions
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12
modules/gatk4/markduplicatesspark/main.nf
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@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES_SPARK {
tag "$meta.id" tag "$meta.id"
label 'process_high' 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" 'broadinstitute/gatk:4.2.3.0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)
@ -22,7 +22,7 @@ process GATK4_MARKDUPLICATES_SPARK {
script: script:
def args = task.ext.args ?: '' 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 input_list = bam.collect{"--input $it"}.join(' ')
def avail_mem = 3 def avail_mem = 3
@ -32,6 +32,10 @@ process GATK4_MARKDUPLICATES_SPARK {
avail_mem = task.memory.giga avail_mem = task.memory.giga
} }
""" """
export SPARK_USER=spark3
gatk --java-options "-Xmx${avail_mem}g" MarkDuplicatesSpark \\ gatk --java-options "-Xmx${avail_mem}g" MarkDuplicatesSpark \\
$input_list \\ $input_list \\
--output $prefix \\ --output $prefix \\