From f169a10b44c960d5d61bfc0d717f8a3500fa9c45 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Sun, 29 Mar 2026 11:54:54 +0100
Subject: [PATCH 1/2] Unnecessary mentions of nf-core

---
 nf_core/pipeline-template/.github/workflows/branch.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/.github/workflows/branch.yml b/nf_core/pipeline-template/.github/workflows/branch.yml
index 3cf6e66abb..b685bc0df4 100644
--- a/nf_core/pipeline-template/.github/workflows/branch.yml
+++ b/nf_core/pipeline-template/.github/workflows/branch.yml
@@ -11,7 +11,7 @@ jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      # PRs to the {{name}} repo main/master branch are only ok if coming from its `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == '{{ name }}'
         run: |

From d2ea5a979579e7300514f49435c247fe3a5b30e9 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Sun, 29 Mar 2026 12:28:45 +0100
Subject: [PATCH 2/2] Jinja template bugfix

Some GHA variables had been introduced between the endif and the if
---
 .../pipeline-template/.github/workflows/download_pipeline.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
index 110d2769a4..4ec8b73824 100644
--- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
+++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
@@ -32,7 +32,7 @@ jobs:
         run: |
           echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
           echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
-          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT{% endraw %}"
+          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
 
   download:
     runs-on: ubuntu-latest
@@ -71,7 +71,7 @@ jobs:
 
       - name: Download the pipeline
         env:
-          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images{% raw %}
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
         run: |
           nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \
           --revision ${{ needs.configure.outputs.REPO_BRANCH }} \