From 76ac145edee3cc5ee8e60c3959dba41e296d66ab Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 9 Dec 2024 15:23:20 +0100 Subject: [PATCH] remove mention of GRCh37 from template if igenomes is skipped closes #3322 --- nf_core/pipeline-template/docs/usage.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/docs/usage.md b/nf_core/pipeline-template/docs/usage.md index 16e6220aaf..85f119e04b 100644 --- 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 -%} <...> ```