Control-FREEC improvements #196
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Prepare release 2.5.1
Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
maxulysse
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Apr 24, 2020
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| if(params.normal_pileup && params.tumor_pileup) // we already have pileups | ||
| """ | ||
| touch ${prefix}${idSample}.pileup |
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Not sure I understand the idea here
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So instead of a useless process here and in the next one, I think we make a new channel that match the ControlFreec process with the input mpileups and make it conditional so we don't even use these two processes at all.
That would be better, and safer, and easier to understand
maxulysse
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maxulysse
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maxulysse
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maxulysse
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maxulysse
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maxulysse
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maxulysse
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maxulysse
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| samtools mpileup \ | ||
| -f ${fasta} ${bam} \ | ||
| ${intervalsOptions} \ | ||
| | bgzip --threads ${task.cpus} -c > ${prefix}${idSample}.pileup.gz | ||
| ${intervalsOptions} > ${prefix}${idSample}.pileup # | bgzip --threads ${task.cpus} -c > ${prefix}${idSample}.pileup.gz |
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if the output is not with the .gz I don't think we're saving it in the results folder actually.
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You are right, have to be fixed in the publishDir as I see
maxulysse
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| return "--" |
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Because I could not see the debug messages. Will be restored eventually :)
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nf-core/sarek pull request
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