Merge pull request nf-core#3330 from mashehu/skip-GRCh37

Template: Remove mention of GRCh37 if igenomes is skipped
sanger-tol · Dec 9, 2024 · 4ea867a · 4ea867a
2 parents 3f85556 + 8c9888b
commit 4ea867a
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -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
 

diff --git a/nf_core/pipeline-template/docs/usage.md b/nf_core/pipeline-template/docs/usage.md
@@ -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.
@@ -93,7 +93,9 @@ with:
 ```yaml title="params.yaml"
 input: './samplesheet.csv'
 outdir: './results/'
+{% if igenomes -%}
 genome: 'GRCh37'
+{% endif -%}
 <...>
 ```