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diminish memory demand (#1872)

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* diminish memory demand

Kallisto was being told to ask for the same amount of memory as it was said for nextflow to limit.

So, when kallisto tried to use it, nextflow was killing it. Thus, diminishing it per 1 GB solved the issue.

* fix prettier

* removing TODOs
This commit is contained in:
Felipe Marques de Almeida 2022-07-12 15:53:02 +02:00 committed by GitHub
parent 589f39c39e
commit ec806cebf1
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2 changed files with 3 additions and 1 deletions
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3
modules/kallistobustools/count/main.nf
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@ -27,6 +27,7 @@ process KALLISTOBUSTOOLS_COUNT {
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def cdna = t1c ? "-c1 $t1c" : '' def cdna = t1c ? "-c1 $t1c" : ''
def introns = t2c ? "-c2 $t2c" : '' def introns = t2c ? "-c2 $t2c" : ''
def memory = task.memory.toGiga() - 1
""" """
kb \\ kb \\
count \\ count \\
@ -39,7 +40,7 @@ process KALLISTOBUSTOOLS_COUNT {
$args \\ $args \\
-o ${prefix}.count \\ -o ${prefix}.count \\
${reads.join( " " )} \\ ${reads.join( " " )} \\
-m ${task.memory.toGiga()}G -m ${memory}G
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

1
tests/modules/kallistobustools/count/test.yml
View file

@ -25,6 +25,7 @@
md5sum: b853330f160e06fc8af170a837384ef5 md5sum: b853330f160e06fc8af170a837384ef5
- path: output/kallistobustools/test.count/kb_info.json - path: output/kallistobustools/test.count/kb_info.json
- path: output/kallistobustools/test.count/matrix.ec - path: output/kallistobustools/test.count/matrix.ec
md5sum: 44eb94feb333b70cd3e55b6f4c0a43db
- path: output/kallistobustools/test.count/output.bus - path: output/kallistobustools/test.count/output.bus
md5sum: f5d8efa83f107826824292cbbdb4e37b md5sum: f5d8efa83f107826824292cbbdb4e37b
- path: output/kallistobustools/test.count/output.unfiltered.bus - path: output/kallistobustools/test.count/output.unfiltered.bus