8000 fix(component): fix included component names for external orgs by prototaxites · Pull Request #4531 · nf-core/tools · GitHub
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fix(component): fix included component names for external orgs - #4531

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prototaxites wants to merge 7 commits into
nf-core:devfrom
prototaxites:fix_included_components
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fix(component): fix included component names for external orgs#4531
prototaxites wants to merge 7 commits into
nf-core:devfrom
prototaxites:fix_included_components

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@prototaxites
@prototaxites prototaxites commented Oct 20, 2026 •
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Perhaps one to discuss exactly how this works, but when linting subworkflows, included component names get garbled if they are from an external organisation - for example, in our sanger-tol org:

include { SAMTOOLS_FAIDX    } from '../../../modules/nf-core/samtools/faidx/main'
include { SAMTOOLS_MERGE    } from '../../../modules/nf-core/samtools/merge/main'
include { SAMTOOLS_MERGEDUP } from '../../../modules/sanger-tol/samtools/mergedup/main'

Returns component names:

subworkflows/../../../modules/nf-core/samtools/faidx
subworkflows/../../../modules/nf-core/samtools/merge
samtools/mergedup

Currently this PR fixes this so we get correct component names, but appends external org names in case of namespace clashes.

samtools/mergedup
nf-core/samtools/faidx
nf-core/samtools/merge
nf-core/subworkflows/bam_samtools_sort_stats

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

@codecov
codecov Bot commented Oct 20, 2026 •
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.65%. Comparing base (654b62c) to head (fbb2b24).

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@prototaxites prototaxites changed the title fix: fix included component names fix(component): fix included component names Oct 20, 2026
@prototaxites prototaxites changed the title fix(component): fix included component names fix(component): fix included component names for external orgs Oct 20, 2026
@mashehu mashehu added this to the 4.3.0 milestone Oct 20, 2026
@mashehu
mashehu force-pushed the fix_included_components branch 2 times, most recently from 3e7e341 to 8f0c758 Compare October 29, 2026 11:00
@mashehu
mashehu force-pushed the fix_included_components branch from 9da0a50 to fbb2b24 Compare October 30, 2026 09:51

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@prototaxites @mashehu
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