Merge pull request #474 from nf-core/fix_rnaseqmetrics_mem

update collectrnaseqmetrics memory requirement

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
 

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} \\