From 141d07cbe3beaf34899fed6120efac17e7e56a8e Mon Sep 17 00:00:00 2001
From: Steven Sutcliffe <sgsutcliffe@gmail.com>
Date: Thu, 10 Oct 2024 16:23:08 -0400
Subject: [PATCH] Fixing linting issue

---
 .github/workflows/linting.yml         | 21 ++++++++++++++++++---
 .github/workflows/linting_comment.yml |  2 +-
 .nf-core.yml                          |  3 +++
 3 files changed, 22 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 8b60f35..a502573 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -1,6 +1,6 @@
 name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
-# It runs the `nf-core lint` and markdown lint tests to ensure
+# It runs the `nf-core pipelines lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
 on:
   push:
@@ -41,18 +41,33 @@ jobs:
           python-version: "3.12"
           architecture: "x64"
 
+      - name: read .nf-core.yml
+        uses: pietrobolcato/action-read-yaml@1.1.0
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yml
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
-      - name: Run nf-core lint
+      - name: Run nf-core pipelines lint
+        if: ${{ github.base_ref != 'master' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
         run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
+      - name: Run nf-core pipelines lint --release
+        if: ${{ github.base_ref == 'master' }}
+        env:
+          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+        run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+
       - name: Save PR number
         if: ${{ always() }}
         run: echo ${{ github.event.pull_request.number }} > PR_number.txt
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 40acc23..42e519b 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
+        uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.nf-core.yml b/.nf-core.yml
index e7be709..7c752f9 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -27,6 +27,9 @@ lint:
     - custom_config
     - manifest.name
     - manifest.homePage
+    - params.max_cpus
+    - params.max_memory
+    - params.max_time
   readme:
     - nextflow_badge