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diminish memory demand (#1872)
* 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
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2 changed files with 3 additions and 1 deletions
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@ -27,6 +27,7 @@ process KALLISTOBUSTOOLS_COUNT {
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def prefix = task.ext.prefix ?: "${meta.id}"
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def cdna = t1c ? "-c1 $t1c" : ''
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def introns = t2c ? "-c2 $t2c" : ''
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def memory = task.memory.toGiga() - 1
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"""
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kb \\
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count \\
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@ -39,7 +40,7 @@ process KALLISTOBUSTOOLS_COUNT {
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$args \\
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-o ${prefix}.count \\
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${reads.join( " " )} \\
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-m ${task.memory.toGiga()}G
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-m ${memory}G
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -25,6 +25,7 @@
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md5sum: b853330f160e06fc8af170a837384ef5
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- path: output/kallistobustools/test.count/kb_info.json
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- path: output/kallistobustools/test.count/matrix.ec
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md5sum: 44eb94feb333b70cd3e55b6f4c0a43db
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- path: output/kallistobustools/test.count/output.bus
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md5sum: f5d8efa83f107826824292cbbdb4e37b
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- path: output/kallistobustools/test.count/output.unfiltered.bus
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