diff --git a/software/gatk/createsequencedictionary/main.nf b/software/gatk/createsequencedictionary/main.nf index bb1d7e96..f6350226 100644 --- a/software/gatk/createsequencedictionary/main.nf +++ b/software/gatk/createsequencedictionary/main.nf @@ -27,10 +27,17 @@ process GATK_CREATESEQUENCEDICTIONARY { script: 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 \\ --REFERENCE $fasta \\ + --URI $fasta $options.args echo \$(gatk CreateSequenceDictionary --version 2>&1) | sed 's/^.*(GATK) v//; s/ HTSJDK.*\$//' > ${software}.version.txt diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config index 26e10357..baa83417 100644 --- a/tests/config/nextflow.config +++ b/tests/config/nextflow.config @@ -5,12 +5,6 @@ params { singularity_pull_docker_container = false } -process { - cpus = 2 - memory = 6.GB - time = 48.h -} - if ("$PROFILE" == "singularity") { singularity.enabled = true singularity.autoMounts = true