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update collectrnaseqmetrics memory requirement #474

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merged 6 commits into from
Apr 3, 2024
Merged

update collectrnaseqmetrics memory requirement #474

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ec3e795
update collectrnaseqmetrics memory requirement
rannick Mar 4, 2024
0980e9f
update changelog
rannick Mar 4, 2024
2cea1a4
first step fix
rannick Mar 4, 2024
8f02765
merging
rannick Mar 25, 2024
78a56b3
align {
rannick Apr 3, 2024
2448d7f
Merge branch 'fix_rnaseqmetrics_mem' of https://github.com/nf-core/rn…
rannick Apr 3, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -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

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12 changes: 6 additions & 6 deletions modules/local/picard/collectrnaseqmetrics/main.nf
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Expand Up @@ -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)
Expand Down Expand Up @@ -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} \\
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