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| conda "${moduleDir}/environment.yml" | ||
| container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container | ||
| ? 'https://depot.galaxyproject.org/singularity/percolator:3.7.1--h6351f2a_0' | ||
| : 'biocontainers/percolator:3.7.1--h6351f2a_0'}" |
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| : 'biocontainers/percolator:3.7.1--h6351f2a_0'}" | |
| : 'quay.io/biocontainers/percolator:3.7.1--h6351f2a_0'}" |
was just added yesterday to the template 🙂 #11251
famosab
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famosab
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Hey nice work, I added two comments that you can ignore and one question about the hard-coded args that you should address :)
| --only-psms \\ | ||
| --post-processing-tdc \\ | ||
| --search-input concatenated \\ |
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Why are these commands hard-coded? We usually prefer to allow users to specify them via ${args}, or if need be then via value input channels.
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You are right, will change this for the parameters you highlighted.
As Percolator actually allows lots of output, all specified by filenames: is there a way to set these as well by meta-variables but in the modules.config - or any other useful way?
The outputs I put in there might be the most often used. But if someone wants to percolate on peptide level, this should also be possible to export (by --results-peptides and --decoy-results-peptides, like the --results-psms I already impleemnted).
Or should I create all files and the user decides, which ones to use? Are there any best practices or examples for this (could not find them, yet).
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Added most/all files as output now. Some can be (de-)activated by the ${args}param
| type: file | ||
| description: percolator output file containing the decoys PSMs | ||
| pattern: "*.pout" | ||
| ontologies: [] |
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no ontologies available ? :(
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Added some, where fitting.
Actually, most of the output files are kind of TSVs, but special ones.
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This PR add a new module for Percolator
PR checklist
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda