Fix specified CPUs in piped commands #753
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Is there a check in the code somewhere that |
Thanks for looking @mahesh-panchal ! There isn't a specific check for (1): the number of CPUs is specified with the And for (2) I believe the |
mahesh-panchal
approved these changes
May 21, 2021
Definitely a little embarrassed at not registering that. |
apeltzer
approved these changes
May 24, 2021
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@mahesh-panchal thanks for looking so closely. This was one of those cases where you think 'oh this should be a quick PR', end up doing in a rush, and then miss lots of things 🤦 . I looked a bit more closely now and I think I've caught everything. |
mahesh-panchal
approved these changes
May 26, 2021
main.nf
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| #Run Filtering step | ||
| samtools calmd -b ${bam} ${fasta} | pmdtools --threshold ${params.pmdtools_threshold} ${treatment} ${snpcap} --header | samtools view -@ ${task.cpus - 2} -Sb - > "${libraryid}".pmd.bam | ||
| samtools calmd -b ${bam} ${fasta} | samtools view -h - | pmdtools --threshold ${params.pmdtools_threshold} ${treatment} ${snpcap} --header | samtools view -Sb - > "${libraryid}".pmd.bam |
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Could you not get the output directly from samtools calmd? At the moment you're using the -b flag which produces compressed bam. Does removing the -b give you uncompressed sam with the headers?
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Ok good call, I've tested and that seems to work. However, i've just checked the line history, and going to check with the actual writers of this process that it makes sense. I never used pmdtools mself 😅
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@apeltzer @maxibor @TCLamnidis I've just changed the PMDtools command after suggestions from @mahesh-panchal . Can you check this looks OK with you? I never used
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I tried running a working command locally with and without samtools view, and it would throw an error when the
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That's a very old version of samtools @TCLamnidis . Could you try with the version in eager (I think 1.10). I tried the eager command without -b earlier and it worked....? Also what is -u? That isn't in the eager command is it? |
That tells samtools to output uncompressed bam. It's used when the next tool in the pipe can read bam, but saves time by not going through a compression-decompression step. |
This works for me? Is the |
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I don't think |
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Ok, then given default Will proceed with merge, and someone can complain later if I brake something ;). |
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To close #750
PR checklist
scrape_software_versions.pynf-core lint .).nextflow run . -profile test,docker).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).