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Template: Remove mention of GRCh37 if igenomes is skipped #3330

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Dec 9, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@
- Fix some typos and improve writing in `usage.md` and `CONTRIBUTING.md` ([#3302](https://github.com/nf-core/tools/pull/3302))
- Add `manifest.contributors` to `nextflow.config` ([#3311](https://github.com/nf-core/tools/pull/3311))
- Update template components ([#3328](https://github.com/nf-core/tools/pull/3328))
- Template: Remove mention of GRCh37 if igenomes is skipped ([#3330](https://github.com/nf-core/tools/pull/3330))

### Download

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4 changes: 3 additions & 1 deletion nf_core/pipeline-template/docs/usage.md
Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
The typical command for running the pipeline is as follows:

```bash
nextflow run {{ name }} --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker
nextflow run {{ name }} --input ./samplesheet.csv --outdir ./results {% if igenomes %}--genome GRCh37{% endif %} -profile docker
```

This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
Expand Down Expand Up @@ -93,7 +93,9 @@ with:
```yaml title="params.yaml"
input: './samplesheet.csv'
outdir: './results/'
{% if igenomes -%}
genome: 'GRCh37'
{% endif -%}
<...>
```

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