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Add validation error for incompatible transcript_fasta and additional_fasta params #1633

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pinin4fjords merged 3 commits into from
Nov 25, 2025
Merged

Add validation error for incompatible transcript_fasta and additional_fasta params #1633

pinin4fjords merged 3 commits into from
Nov 25, 2025
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Copilot AI commented Nov 25, 2025 •
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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 nf-core/rnaseq 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).

Description

When users provide both --transcript_fasta and --additional_fasta without a pre-built pseudo-aligner index, the pipeline fails at quantification with a confusing error about missing transcripts. This happens because additional_fasta sequences are appended to genome FASTA/GTF, but the user-provided transcript_fasta is used as-is without the spike-ins.

Changes

  • Validation: Fail fast with clear error when both params are provided AND the pipeline needs to build a pseudo-aligner index
  • Index check: Only check the relevant index for the selected pseudo-aligner (salmon_index for salmon, kallisto_index for kallisto)
  • Documentation: Updated docs/usage.md and schema help text to clarify this incompatibility

The combination remains valid when a pre-built index containing the spike-ins is provided (e.g., test profile provides salmon_index).

Closes #1450

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Copilot AI mentioned this pull request Nov 25, 2025
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Copilot AI changed the title [WIP] Add validation error for incompatible transcript_fasta and additional_fasta params Add validation error for incompatible transcript_fasta and additional_fasta params Nov 25, 2025
Copilot AI requested a review from pinin4fjords November 25, 2025 20:57
@pinin4fjords pinin4fjords marked this pull request as ready for review November 25, 2025 20:58
@pinin4fjords pinin4fjords merged commit 2950beb into fix/transcript-fasta-additional-fasta-validation Nov 25, 2025
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@pinin4fjords pinin4fjords deleted the copilot/sub-pr-1632 branch November 25, 2025 20:58
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github-actions bot commented Nov 25, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4360974

+| ✅ 284 tests passed       |+
#| ❔   8 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/rnaseq/rnaseq/subworkflows/local/prepare_genome/main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2025-11-25 20:56:22

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@pinin4fjords pinin4fjords Awaiting requested review from pinin4fjords

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