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Value channels for the reference and samplesheet; COUNTS_TO_FITNESS version; apptainer for RUN_DIMSUM - #99

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Nov 10, 2026
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Value channels for the reference and samplesheet; COUNTS_TO_FITNESS version; apptainer for RUN_DIMSUM#99
MaximilianStammnitz merged 1 commit into
nf-core:devfrom
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@MaximilianStammnitz MaximilianStammnitz commented Nov 10, 2026

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For @maxulysse's second review on #54.

Value channels instead of per-library broadcasts

The reference FASTA and the samplesheet are one file per run, but they were queue channels, so every process that needed them per library got its own copy through x.combine(per_library).map { it[n] }. They are now value channels (Channel.value(file(...))). As a result, the outputs of BWA_INDEX, DMSANALYSIS_AASEQ, DMSANALYSIS_POSSIBLE_MUTATIONS and EXPDESIGN_FITNESS are value channels too, and all of these broadcasts are removed, in workflows/deepmutscan.nf and in CALCULATE_FITNESS.

Smaller fixes

  • COUNTS_TO_FITNESS.out.versions is now collected
  • RUN_DIMSUM selects the Singularity image for apptainer too, like all other modules
  • An outdated comment in the variant counter now says that indel reads are removed in MERGE_ALIGN. We aim to include indels DMS support in a future release (see In-frame insertion and deletion (indel) variants #88)

PR checklist

  • This comment contains a description of changes (with reason)
  • Make sure your code lints (nf-core pipelines lint)
  • Ensure the test suite passes (nf-test test --profile +docker)
  • CHANGELOG.md update: not needed, these are fixes within v1.0.0

@MaximilianStammnitz
Reference and samplesheet as value channels instead of per-library br…
8b70c22 
…oadcasts; COUNTS_TO_FITNESS version; apptainer image for RUN_DIMSUM; new snapshot
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8b70c22

+| ✅ 243 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   2 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.0.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_unchanged - File ignored due to lint config: assets/nf-core-deepmutscan_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-deepmutscan_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 4.2.1
  • Run at 2026-11-10 12:30:35

@MaximilianStammnitz MaximilianStammnitz added documentation Improvements or additions to documentation enhancement New feature or request labels Nov 10, 2026
@MaximilianStammnitz MaximilianStammnitz mentioned this pull request Nov 10, 2026
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MaximilianStammnitz merged commit 5bcdc2b into nf-core:dev Nov 10, 2026
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