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🚧 Understand how to integrate modules (from nf-core or bigbio)#687

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enryH wants to merge 6 commits intodevfrom
nfcore_thermo_test
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🚧 Understand how to integrate modules (from nf-core or bigbio)#687
enryH wants to merge 6 commits intodevfrom
nfcore_thermo_test

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@enryH
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@enryH enryH commented Mar 13, 2026 •
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See if nf-core/thermorawfileparser works. Since there are now topic channels in nf-core/modules, I need to see how to access the version of thermorawfile parser

  • update to fetch SDRF and FASTA files from maintained repo
  • add back in version of thermorawfileparser

How to create a diff file for local changes to nf-core module:

video: https://www.youtube.com/watch?v=7pu6Ikhi1eU
docs: https://nf-co.re/docs/nf-core-tools/modules/patch

in short nf-core modules patch thermorawfileparser

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the bigbio/quantms branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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coderabbitai bot commented Mar 13, 2026 •
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github-actions bot commented Mar 13, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3c5269f

+| ✅ 110 tests passed       |+
#| ❔  19 tests were ignored |#
!| ❗   3 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/quantms/quantms/subworkflows/local/id/main.nf: _ ch_software_versions = ch_software_versions.mix(PHOSPHO_SCORING.out.versions.ifEmpty(null))
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/quantms/quantms/subworkflows/local/dda_id/main.nf: _ ch_software_versions = ch_software_versions.mix(PHOSPHO_SCORING.out.versions.ifEmpty(null))
    _

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-03-17 07:18:41

@enryH enryH changed the title 🔧 update to fetch SDRF and FASTA files from maintained repo 🚧 Understand how to integrate modules (from nf-core or bigbio) Mar 16, 2026
@ypriverol
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ypriverol commented Mar 17, 2026

@enryH I will prefer to use our thermorawfileparser https://github.com/bigbio/nf-modules/tree/main/modules/bigbio/thermorawfileparser is that is possible.

@enryH
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enryH commented Mar 17, 2026

@enryH I will prefer to use our thermorawfileparser https://github.com/bigbio/nf-modules/tree/main/modules/bigbio/thermorawfileparser is that is possible.

I will update the bigbio version to match the nf-core version. But thermorawfileparser is maintained on nf-core/modules, so I thought to go for that option.

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ypriverol commented Mar 17, 2026

I saw the PR in bigbio/nf-modules it is nice for thermorawfileparser as soon as is updated I can merge the PR. We are using also mgf for the relink pipeline also.

@enryH
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enryH commented Mar 17, 2026

Any idea why there are staging errors? (link)

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@enryH @ypriverol