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remove mention of GRCh37 from template if igenomes is skipped
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mashehu committed Dec 9, 2024
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4 changes: 3 additions & 1 deletion nf_core/pipeline-template/docs/usage.md
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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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