From f1aa3f9ff6a2ece6f1455fd7362e765972d35ca9 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 11 Oct 2024 16:17:08 +0200
Subject: [PATCH] fix linting with gitignore

---
 .../workflows/template_version_comment.yml    | 22 ++++++++++---------
 .gitignore                                    |  2 +-
 2 files changed, 13 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml
index 9dea41f..d67ee08 100644
--- a/.github/workflows/template_version_comment.yml
+++ b/.github/workflows/template_version_comment.yml
@@ -10,9 +10,11 @@ jobs:
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
 
       - name: Read template version from .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.0.0
+        uses: nichmor/minimal-read-yaml@v0.0.2
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
@@ -21,23 +23,23 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
-
       - name: Check nf-core outdated
         id: nf_core_outdated
-        run: pip list --outdated | grep nf-core
+        run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV}
 
       - name: Post nf-core template version comment
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         if: |
-          ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core'
+          contains(env.OUTPUT, 'nf-core')
         with:
           repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
           allow-repeats: false
           message: |
-            ## :warning: Newer version of the nf-core template is available.
-
-            Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
-            Please update your pipeline to the latest version.
-
-            For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
+            > [!WARNING]
+            > Newer version of the nf-core template is available.
+            >
+            > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
+            > Please update your pipeline to the latest version.
+            >
+            > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
           #
diff --git a/.gitignore b/.gitignore
index 792b37f..2eef655 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,4 @@
 .nextflow*
-.nf-test*
 work/
 data/
 results/
@@ -7,3 +6,4 @@ results/
 testing/
 testing*
 *.pyc
+.nf-test*