🛠️ Modification to bin cobalt outputs and add purity forcing #3
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| -ref_genome_version ${params.genomeVersion} | ||
| if [ -f "${params.outdir}/amber/${tumor}.amber.baf.tsv.gz" ] && \ | ||
| [ -f "${params.outdir}/amber/${tumor}.amber.baf.pcf" ] && \ | ||
| [ -f "${params.outdir}/amber/${tumor}.amber.qc" ]; then |
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These checks are managed by nextflow. If nextflow sees the outputs you expect in a previous run, it will cached these step.
Was this not happening for you?
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This is part of the updates for the force -- because the workflow has finished completely the runDir is already copied to the publishDir and it goes to redo these steps since the output files don't exist in the new runDir.
main.nf
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| last_idx = cobalt_ratio_pcf_probes_logR.index[-1] | ||
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| cobalt_ratio_pcf_probes_logR.to_csv("${tumor}.cobalt.ratio.pcf", sep='\\t', index=False) | ||
| """ |
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Add here some """.stripIndent() to the script so the script is properly indented when added to a file.
See the other processes.
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Thanks I missed this -- surprised this didn't cause an error.
| @@ -1,4 +1,5 @@ | |||
| params.cores = 4 | |||
| params.cores = 1 | |||
| params.memory = '4 GB' | |||
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Im thinking about keeping 32 GB, and use 4 GB for testing in nf.test:
params {
memory = '4 GB'
tumor = "TEST"
binProbes = 100
binLogR = 0.5
cobalt_ratio_pcf = "${projectDir}/tests/outdir/cobalt/TEST.cobalt.ratio.pcf"
cobalt_ratio_tsv = "${projectDir}/tests/outdir/cobalt/TEST.cobalt.ratio.tsv.gz"
}Unless you think it doesn't need that much memory by default?
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I ended up adding a memory parameter because it seems sample/system dependent. I prefer to keep it low and then configure it higher on samples or systems where necessary but either way works.
Several modifications in order to improve workflow for routine use.