Decoupling cometconfig and update comet to nf-core version - #15
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Pull request overview
This PR updates the Comet integration to version 2026.01.1 and decouples Comet parameter templating into a dedicated COMETCONFIG module, allowing a user-provided template (or bundled default) to be adjusted before running Comet.
Changes:
- Add
comet_config_templatepipeline parameter and plumb it throughmain.nf→workflows/mspepid.nf→SPECTRA_IDENTIFICATION. - Introduce
modules/local/cometconfigto generate adjusted*.comet.paramsfiles from a template. - Update Comet module to consume a params file and bump Comet to
2026.01.1(conda + container), including version-capture fixes.
Reviewed changes
Copilot reviewed 12 out of 12 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| workflows/mspepid.nf | Adds comet_config_template to workflow inputs and forwards it to spectra identification |
| subworkflows/local/spectra_identification/main.nf | Wires COMETCONFIG into the Comet execution path and passes generated params to Comet |
| nextflow_schema.json | Adds schema entry for comet_config_template |
| nextflow.config | Adds default params.comet_config_template = null |
| modules/local/cometconfig/main.nf | New module that copies a template and applies tolerance edits via sed |
| modules/local/cometconfig/environment.yml | Conda env for COMETCONFIG |
| modules/local/comet/main.nf | Updates Comet container/conda version; changes input to accept a params file |
| modules/local/comet/environment.yml | Bumps comet-ms conda package version |
| modules/local/comet/meta.yml | Adjusts Comet version-eval command (but docs now need updating for new inputs) |
| conf/modules.config | Disables publishing for COMETCONFIG |
| assets/searchengines/comet.params | Adds bundled default Comet params template |
| main.nf | Forwards params.comet_config_template into the main workflow call |
Comments suppressed due to low confidence (1)
modules/local/comet/main.nf:18
COMEToutputspath("*.comet.params"), but the script copies the stagedcomet_paramsfile to${prefix}.comet.paramswhen names differ. That can leave two*.comet.paramsfiles in the work dir (e.g.default.comet.params+sample.comet.params), so the output may become a list unexpectedly and break downstream usage. Emit only the intended params file (exact filename) and/or remove/rename the staged input after copying so only one match remains.
tuple val(meta), path(mzml), path(fasta), path(comet_params)
output:
tuple val(meta), path("*.comet.params"), emit: params
tuple val(meta), path("*.sqt"), emit: sqt, optional: true
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julianu
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Pull request overview
Copilot reviewed 17 out of 17 changed files in this pull request and generated 3 comments.
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di-hardt
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Apr 2, 2026
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works fine with and without given comet parameter file
di-hardt
approved these changes
Apr 2, 2026
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This pull request introduces a new modular approach for handling Comet MS/MS search engine configuration in the workflow. The main changes include splitting the Comet parameter file generation into a dedicated
COMETCONFIGprocess, updating related workflow and configuration files, and improving output management for both Comet and Percolator modules.The most important changes are:
These changes make the workflow more modular, maintainable, and easier to configure for different Comet search scenarios.