fix linting

wsjung · Feb 21, 2024 · 9d3f38f · 9d3f38f
1 parent 0044859
commit 9d3f38f
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Showing 15 changed files with 138 additions and 47 deletions.
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
@@ -19,7 +19,7 @@ jobs:
             # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
             - name: Post PR comment
               if: failure()
-              uses: mshick/add-pr-comment@v2
+              uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
               with:
                   message: |
                       ## This PR is against the `master` branch :x:

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -14,10 +14,10 @@ jobs:
     pre-commit:
         runs-on: ubuntu-latest
         steps:
-            - uses: actions/checkout@v4
+            - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
             - name: Set up Python 3.11
-              uses: actions/setup-python@v5
+              uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
               with:
                   python-version: 3.11
                   cache: "pip"
@@ -32,12 +32,12 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Check out pipeline code
-              uses: actions/checkout@v4
+              uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
             - name: Install Nextflow
-              uses: nf-core/setup-nextflow@v1
+              uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
 
-            - uses: actions/setup-python@v5
+            - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
               with:
                   python-version: "3.11"
                   architecture: "x64"
@@ -60,7 +60,7 @@ jobs:
 
             - name: Upload linting log file artifact
               if: ${{ always() }}
-              uses: actions/upload-artifact@v4
+              uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
               with:
                   name: linting-logs
                   path: |

diff --git 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@v3
+              uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # 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@v2
+              uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
               with:
                   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
                   number: ${{ steps.pr_number.outputs.pr_number }}

diff --git a/modules.json b/modules.json
@@ -7,17 +7,17 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
+                        "git_sha": "de45447d060b8c8b98575bc637a4a575fd0638e1",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9",
+                        "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
+                        "git_sha": "ccacf6f5de6df3bc6d73b665c1fd2933d8bbc290",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test