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Document reference selection for consuming pipelines #167

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Document reference selection for consuming pipelines #167

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9e5e044
Document reference selection for consuming pipelines
maxulysse Oct 24, 2026
7a7c66b
Merge branch 'dev' into docs/reference-selection
maxulysse Oct 24, 2026
ec235d0
Clarify per-key reference resolution in usage docs
maxulysse Oct 28, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -71,6 +71,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#164](https://github.com/nf-core/references/pull/164) - Replace `update_references_file` string rewriting with nf-schema `allowParamsSubstitution`, so datasheets can carry `${params.references_base_path}` placeholders
- [#165](https://github.com/nf-core/references/pull/165) - Document `--references_base_path`, multiple genomes, and the asset file format in `docs/usage.md`
- [#166](https://github.com/nf-core/references/pull/166) - Rename the datasheet `source`, `source_version`, and derived `source_vcf` meta fields to `reference_source`, `annotation_version`, and `annotation_source` (#65)
- [#167](https://github.com/nf-core/references/pull/167) - Document reference selection precedence for consuming pipelines in `docs/usage.md`

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11 changes: 11 additions & 0 deletions docs/usage.md
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Expand Up @@ -388,3 +388,14 @@ We recommend adding the following line to your environment to limit this (typica
```bash
NXF_OPTS='-Xms1g -Xmx4g'
```

## Reference selection in consuming pipelines

A pipeline that consumes these references resolves each key, such as `fasta` or `fasta_fai`, separately. Each key takes its value from the first source in this order that supplies it:

1. Explicit parameters, for example `--fasta` and `--fasta_fai`.
2. One references datasheet or one iGenomes catalogue entry. The datasheet is passed as a file, or located from a base URL plus a genome key. Selecting both a datasheet and a catalogue entry is an error.

An explicit `--fasta` with no `--fasta_fai` therefore takes `fasta_fai` from the datasheet or catalogue entry.

Each consuming pipeline names its own parameters for these sources and documents them in its usage pages. See the [nf-core/bamtofastq usage documentation](https://nf-co.re/bamtofastq/usage) for an example.
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