Installed the fasta_classify_catpack subworkflow#38
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KateSakharova merged 4 commits intodevfrom Mar 16, 2026
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.5.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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KateSakharova
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Mar 13, 2026
| // Database preparation | ||
| // | ||
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| // Handle pre-built db: untar if compressed, or use directory directly |
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@mberacochea that part was not working for input as directory. Directory doesn't have .name in nextflow. I have fixed it by checking instance. Maybe push that fix to nf-core 😱
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OK, I'll fix it there. Can you create the patch please?
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Later.. I'm still testing.
One more note: we need to check input DB directory for structure. You are expecting db and tax subfolders inside. It is not obvious and should be checked and described in subwf
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ochkalova
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Mar 16, 2026
conf/modules.config
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| withName: 'CATPACK_ADDNAMES_BINS' { | ||
| ext.args = '--only_official' | ||
| publishDir = [ | ||
| path: { "${params.outdir}/${params.mode}/taxonomy" }, | ||
| mode: params.publish_dir_mode, | ||
| pattern: "*bin2classification*.txt", | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } |
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This publishDir won't work because file is currently called "${meta.id}".txt
conf/modules.config
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| withName: 'CATPACK_SUMMARISE_BINS' { | ||
| ext.prefix = "bins_summary" | ||
| publishDir = [ | ||
| path: { "${params.outdir}/${params.mode}/taxonomy" }, | ||
| mode: params.publish_dir_mode, | ||
| pattern: "*_summary.txt", | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } |
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Do you think we need to run this module? I think it's unnecessary...
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I was not sure about it... I can make it 'false'
| """ | ||
| input[0] = [ | ||
| [ id: 'test' ], | ||
| file("${projectDir}/modules/local/rename_fasta_for_catpack/tests/test.fasta", checkIfExists: true) |
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| file("${projectDir}/modules/local/rename_fasta_for_catpack/tests/test.fasta", checkIfExists: true) | |
| file("${moduleDir}/tests/test.fasta", checkIfExists: true) |
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| script: | ||
| def is_compressed = fasta.name.endsWith('.gz') | ||
| extension = '.fasta' | ||
| def base = fasta.name | ||
| .replaceAll(/\.gz$/, '') | ||
| .replaceAll(/\.(fa|fasta|fna)$/, '') | ||
| def output_name = base + extension | ||
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| if (is_compressed) { | ||
| """ | ||
| mkdir -p output | ||
| gunzip -c ${fasta} > output/${output_name} | ||
| """ | ||
| } else { | ||
| """ | ||
| mkdir -p output | ||
| ln -s ../${fasta} output/${output_name} | ||
| """ | ||
| } |
| tuple val(meta), path(fasta) | ||
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| output: | ||
| tuple val(meta), path("output/*.fasta{,.gz}"), emit: renamed_fasta |
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You uncompress all gz, so it's always just .fasta
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| - "output/*.fasta{,.gz}": | ||
| type: file | ||
| description: | | ||
| Renamed FASTA file with a .fasta extension, decompressed if the input was compressed. | ||
| pattern: "output/*.fasta{,.gz}" |
nextflow.config
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| // NCBI taxonomy | ||
| cat_db = null | ||
| cat_db_download_id = '' |
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Why '' and not null? Why it doesn't have default value like checkm2_db_zenodo_id?
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because I didn't search for it... 🤦♀️
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Taxonomy part
fasta_classify_catpackfrom nf-core.fastaextension required for CAT_pack as input