From 76ac145edee3cc5ee8e60c3959dba41e296d66ab Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 9 Dec 2024 15:23:20 +0100
Subject: [PATCH 1/3] 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 -%}
 <...>
 ```
 

From e073622e8bdfb1879eb38fc981cf931152322aac Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 9 Dec 2024 15:23:56 +0100
Subject: [PATCH 2/3] add missing closing tag

---
 nf_core/pipeline-template/.gitpod.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml
index b8165fbc06..1a0c9f2a83 100644
--- a/nf_core/pipeline-template/.gitpod.yml
+++ b/nf_core/pipeline-template/.gitpod.yml
@@ -9,3 +9,4 @@ vscode:
   extensions:
     #{%- if code_linters -%}
     - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack
+    #{%- endif -%}

From 1da1fc600271fccdccc41b4c1cb8f5724a85c148 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 9 Dec 2024 15:27:29 +0100
Subject: [PATCH 3/3] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0eacaed176..10f847ed2a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -75,6 +75,7 @@
 - Parallelize pipeline GHA tests over docker/conda/singularity ([#3214](https://github.com/nf-core/tools/pull/3214))
 - Fix `template_version_comment.yml` github action ([#3212](https://github.com/nf-core/tools/pull/3212))
 - Fix pre-commit linting on pipeline template ([#3218](https://github.com/nf-core/tools/pull/3218))
+- Template: Remove mention of GRCh37 if igenomes is skipped ([#3330](https://github.com/nf-core/tools/pull/3330))
 
 ### Linting