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Replace .out channel access with typed workflow return assignment - #157

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feat/typed-workflows
Sep 24, 2026
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Replace .out channel access with typed workflow return assignment#157
maxulysse merged 1 commit into
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feat/typed-workflows

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@maxulysse maxulysse commented Sep 24, 2026 •
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Replaces every legacy .out. channel access with named access on the captured invocation result across main.nf, workflows/references.nf, prepare_genome_dnaseq and prepare_genome_rnaseq.

This is the next step towards full typed workflows (Phase 3 Part A, nf-core/rnaseq#1935), unblocking typed take:/typing of nested workflows, since .out is not supported by typed workflows.

Each process and subworkflow invocation is captured in a channel variable and its named outputs are referenced on it (e.g. ch_faidx.fai instead of SAMTOOLS_FAIDX.out.fai).

Verified: nextflow lint and nf-core pipelines lint clean; default, htslib (x2) and hisat2 (x4) nf-tests pass with unchanged snapshots.

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Verified by @maxulysse

@maxulysse
refactor: replace dot-out access with typed workflow return assignment
3709282 
Access process and workflow output channels through the return value of
the invocation instead of the legacy dot-out channel access, which is
not supported by typed workflows.

Every process and subworkflow invocation is captured in a channel
variable and its named outputs are referenced on it (for example
ch_faidx.fai instead of SAMTOOLS_FAIDX.out.fai), in main.nf,
workflows/references.nf, prepare_genome_dnaseq and prepare_genome_rnaseq.

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@maxulysse maxulysse changed the title Replace channel access with typed workflow return assignment Replace .out channel access with typed workflow return assignment Sep 24, 2026
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3709282

+| ✅ 216 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   8 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • 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 output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 4.1.0
  • Run at 2026-09-24 11:01:28

@maxulysse
maxulysse merged commit e0f4e7e into dev Sep 24, 2026
32 of 36 checks passed
@maxulysse
maxulysse deleted the feat/typed-workflows branch September 24, 2026 11:40
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