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Document asset input in usage docs - #165

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maxulysse merged 1 commit into
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docs/asset-input
Oct 23, 2026
Merged

Document asset input in usage docs#165
maxulysse merged 1 commit into
devfrom
docs/asset-input

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@maxulysse

@maxulysse maxulysse commented Oct 23, 2026

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PR checklist

  • This comment contains a description of changes (for why/what changed, see CONTRIBUTING.md)
  • Container version(s) are updated/rebuilt and pin changed software (if needed)
  • CHANGELOG.md is updated
  • nextflow_schema.json is updated (if needed)
  • docs/usage.md is updated (if needed)
  • docs/output.md is updated (if needed)
  • assets/ is updated (if needed)
  • Remove all TODO comments
  • Test this locally and/or on CI (particularly with GPU/singularity tests)
  • For modules: nf-core/modules PR along with basic tests on Linux, macOS and Windows
  • For pipelines: template update at nf-core/tools along with basic tests (stub run on all profiles)

Description

Fills the two placeholder sections under Asset input in docs/usage.md, both of which rendered a bare TODO on the website.

Multiple genomes states that a datasheet is a YAML list with one entry per genome and that genome is the only required field. It explains why species and source must be set, since the pipeline builds the published path from species/source/genome, and shows a two-entry example with the output tree it produces. It also records that run flags are computed per entry, so genomes with different capabilities build independently in one run.

Full asset file gives a worked example over real GRCh37decoy paths covering genome and annotation fields, a prebuilt index, and a GATK resource VCF with its tabix index and provenance, then lists the format rules. Supplying an artefact stops the pipeline building it, which I verified against the run_X: meta.X ? false : true flags in datasheet_to_channel. The vcf_*_vcf fields take a path or a list, the TBI list pairs by position, and a null entry means the pipeline builds that index. The *_source fields become the Annotation/<source> segment of the published path.

The example assets link moves under Full asset file. It previously sat after two empty headings, so it read as the conclusion of a section that still said TODO.

This PR also replaces an em dash and an en dash. Both are non-ASCII and banned by the repository prose rules. The earlier deslop pass covered the roadmap and the PR bodies but not docs/.

Not changed

Line 9 keeps the template's <!-- TODO nf-core: ... --> comment. It is tracked upstream, so removing it locally would be reverted by the next template sync. pipeline_todos still reports it, which is why nf-core pipelines lint stays at 21 warnings: that check matches TODO nf-core: markers, so the two bare TODOs removed here were never counted.

Testing

  • prek passes, including prettier.
  • nf-core pipelines lint: 366 passed, 0 failed, 21 pre-existing warnings.
  • Both datasheet URLs added return HTTP 200.
  • Docs only. No Nextflow code changed, so the test suite is unaffected and was not rerun.

Generated by OpenCode

@maxulysse
Document asset input in usage docs
648f358 
Fill the Multiple genomes and Full asset file placeholders, and move
the example assets link under the heading it belongs to.

Also replace an em dash and an en dash, both non-ASCII and banned by
the repository prose rules.

Generated by OpenCode
@github-actions

github-actions Bot commented Oct 23, 2026

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.1.0.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

@github-actions

github-actions Bot commented Oct 23, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 648f358

+| ✅ 219 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 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 base.config: Check the defaults for all processes
  • 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 output.md: Write this documentation describing your workflow's output

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 4.1.0
  • Run at 2026-10-23 09:13:32

@maxulysse
maxulysse merged commit 9895b75 into dev Oct 23, 2026
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@maxulysse
maxulysse deleted the docs/asset-input branch October 23, 2026 09:56
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