Added parameter filter_genes_by_aa_length #127
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Can you kindly do, git fetch upstream
git fetch origin
git checkout feat/filter_genes_by_aa_length
./pfr_genepalto resume your previous run with the updated code and check if you get the desired effects from the Please don't mid going through the PR code changes and highlight anything that sticks out. Many Thanks! |
GallVp
commented
Dec 11, 2024
| @@ -240,6 +240,10 @@ process { // SUBWORKFLOW: GFF_MERGE_CLEANUP | |||
| ext.prefix = { "${meta.id}.liftoff.braker" } | |||
| } | |||
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| withName: '.*:GFF_MERGE_CLEANUP:FILTER_BY_ORF_SIZE' { | |||
| ext.args = params.filter_genes_by_aa_length ? "--no-pseudo --keep-genes -C -l ${params.filter_genes_by_aa_length * 3}" : '' | |||
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params.filter_genes_by_aa_length is multiplied by 3 to get the CDS length for the -l parameter.
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Hey @rosscrowhurst Here is another attempt at solving the same problem. Please update your clone once again and try another resume. Many thanks! |
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PR checklist
nf-core pipelines 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).