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fix: remove memory requirements and simplify URI

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This commit is contained in:
MaxUlysse 2021-02-16 13:54:40 +01:00
parent 30e3f2c5f5
commit 28dc9227d7
2 changed files with 8 additions and 7 deletions
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9
software/gatk/createsequencedictionary/main.nf
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@ -27,10 +27,17 @@ process GATK_CREATESEQUENCEDICTIONARY {
script: script:
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
def avail_mem = 6
if (!task.memory) {
log.info '[GATK] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
""" """
gatk --java-options "-Xmx${task.memory.toGiga()}g" \\ gatk --java-options "-Xmx${avail_mem}g" \\
CreateSequenceDictionary \\ CreateSequenceDictionary \\
--REFERENCE $fasta \\ --REFERENCE $fasta \\
--URI $fasta
$options.args $options.args
echo \$(gatk CreateSequenceDictionary --version 2>&1) | sed 's/^.*(GATK) v//; s/ HTSJDK.*\$//' > ${software}.version.txt echo \$(gatk CreateSequenceDictionary --version 2>&1) | sed 's/^.*(GATK) v//; s/ HTSJDK.*\$//' > ${software}.version.txt

6
tests/config/nextflow.config
View file

@ -5,12 +5,6 @@ params {
singularity_pull_docker_container = false singularity_pull_docker_container = false
} }
process {
cpus = 2
memory = 6.GB
time = 48.h
}
if ("$PROFILE" == "singularity") { if ("$PROFILE" == "singularity") {
singularity.enabled = true singularity.enabled = true
singularity.autoMounts = true singularity.autoMounts = true