diff --git a/CHANGELOG.md b/CHANGELOG.md index 5ce3a28a..d8815a6e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed - Update to nf-tools 2.11.1 [#457] (https://github.com/nf-core/rnafusion/pull/457) +- Update picard collectrnaseqmetrics memory requirements to 0.8x what is provided [#474](https://github.com/nf-core/rnafusion/pull/474) ### Fixed diff --git a/modules/local/picard/collectrnaseqmetrics/main.nf b/modules/local/picard/collectrnaseqmetrics/main.nf index af0b8958..ede593e0 100644 --- a/modules/local/picard/collectrnaseqmetrics/main.nf +++ b/modules/local/picard/collectrnaseqmetrics/main.nf @@ -2,10 +2,10 @@ process PICARD_COLLECTRNASEQMETRICS { tag "$meta.id" label 'process_medium' - conda "bioconda::picard=3.0.0 r::r-base" + conda "bioconda::picard=3.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' : - 'biocontainers/picard:3.0.0--hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' : + 'biocontainers/picard:3.1.0--hdfd78af_0' }" input: tuple val(meta), path(bam), path(bai) @@ -33,15 +33,15 @@ process PICARD_COLLECTRNASEQMETRICS { def rrna = rrna_intervals == [] ? '' : "--RIBOSOMAL_INTERVALS ${rrna_intervals}" def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def avail_mem = 3 + def avail_mem = 3072 if (!task.memory) { log.info '[Picard CollectRnaMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.mega*0.8).intValue() } """ picard \\ - -Xmx${avail_mem}g \\ + -Xmx${avail_mem}M \\ CollectRnaSeqMetrics \\ --TMP_DIR ./tmp \\ ${strandedness} \\