Fixing more lint tests.

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
+        uses: dawidd6/action-download-artifact@v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
+        uses: marocchino/sticky-pull-request-comment@v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}

pyproject.toml

@@ -3,13 +3,11 @@
 [tool.ruff]
 line-length = 120
 target-version = "py38"
-cache-dir = "~/.cache/ruff"
-
-[tool.ruff.lint]
 select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"]
+cache-dir = "~/.cache/ruff"
 
-[tool.ruff.lint.isort]
+[tool.ruff.isort]
 known-first-party = ["nf_core"]
 
-[tool.ruff.lint.per-file-ignores]
+[tool.ruff.per-file-ignores]
 "__init__.py" = ["E402", "F401"]