Optional bowtie build #6
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While not as elegant as the storeDir solution, I can add another pipeline parameter for the samtools index and add some conditional logic to skip samtools faidx if this is present. What are your thoughts? |
mahesh-panchal
commented
Nov 6, 2024
| @@ -62,8 +62,13 @@ process { | |||
| publishDir = [ enabled: false ] | |||
| } | |||
| withName: 'BOWTIE2_BUILD' { | |||
| // Check if the Bowtie2 index exists and skip if it does | |||
| process.when = !new File(params.bowtie2_db + '.1.bt2').exists() | |||
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This doesn't work. process.when is not a directive. Also conditional execution should be included in the code to make it transparent.
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Okay, I see. I still received an error about bowtie2-build when trying to run with the suggestions you made in this PR, that's why I came up with another suggestion.
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If you have something I can test on, I can make sure it works.
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PR checklist
Partially resolves #4.
Writes out the bowtie2 indices (and versions.yml) to the same directory as the fasta input. If this directory is used again in another run, the cached index will be used instead of rerunning the process.
The same cannot be done for samtools faidx (yet) because it's a separate process which writes it's own versions.yml. These
versions.yml are used later on for collecting versions information. Over the summer, the nf-core modules will go through a restructure making the
versions.ymlobsolete meaning thestoreDirsolution can then be used. It's currently included as a comment.nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).