update actions

Author: mashehu

.github/workflows/codspeed.yml

@@ -28,7 +28,7 @@ jobs:
     name: Run start-up benchmarks
     runs-on: codspeed-macro
     steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
+      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         name: Check out source-code repository
 
       - name: Set up Python

.github/workflows/pr-comment.yml

@@ -58,7 +58,7 @@ jobs:
 
       - name: Post PR comment
         if: steps.meta.outputs.post == 'true'
-        uses: marocchino/sticky-pull-request-comment@70d2764d1a7d5d9560b100cbea0077fc8f633987 # v3
+        uses: marocchino/sticky-pull-request-comment@5770ad5eb8f42dd2c4f34da00c94c5381e49af88 # v3.0.5
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.meta.outputs.pr_number }}

.github/workflows/test_offline_configs.yml

@@ -67,28 +67,28 @@ jobs:
           fetch-depth: "0"
       - name: Check the correct default config base of the nf-core configs
         id: check_default_config
-        uses: GuillaumeFalourd/assert-command-line-output@2cd32f7751887b5ef1886521de68ea2ec3e2aee7 # v2
+        uses: GuillaumeFalourd/assert-command-line-output@63ad23408d758ee7f09b4557cc0901d6ae4f3f76 # v2.4
         with:
           command_line: nextflow config -value params.custom_config_base .
           contains: https://raw.githubusercontent.com/nf-core/configs/master
           expected_result: PASSED
       - name: Check the correct inclusion of an existing institutional profile
         id: check_profile_inclusion
-        uses: GuillaumeFalourd/assert-command-line-output@2cd32f7751887b5ef1886521de68ea2ec3e2aee7 # v2
+        uses: GuillaumeFalourd/assert-command-line-output@63ad23408d758ee7f09b4557cc0901d6ae4f3f76 # v2.4
         with:
           command_line: nextflow config -profile google -o flat .
           contains: "The nf-core framework" # Part of CITATION.cff, should always be printed if profile is included
           expected_result: PASSED
       - name: Check the failed inclusion of a non-existing institutional profile
         id: check_nonexistent_profile
-        uses: GuillaumeFalourd/assert-command-line-output@2cd32f7751887b5ef1886521de68ea2ec3e2aee7 # v2
+        uses: GuillaumeFalourd/assert-command-line-output@63ad23408d758ee7f09b4557cc0901d6ae4f3f76 # v2.4
         with:
           command_line: nextflow config -profile GLaDOS -o flat .
           contains: "Unknown configuration profile: 'GLaDOS'"
           expected_result: PASSED
       - name: Check that offline prevents inclusion of nf-core configs
         id: check_offline_mode
-        uses: GuillaumeFalourd/assert-command-line-output@2cd32f7751887b5ef1886521de68ea2ec3e2aee7 # v2
+        uses: GuillaumeFalourd/assert-command-line-output@63ad23408d758ee7f09b4557cc0901d6ae4f3f76 # v2.4
         env:
           NXF_OFFLINE: true
         with:

nf_core/pipeline-template/.github/actions/nf-test/action.yml

@@ -37,7 +37,7 @@ runs:
 
     - name: Setup apptainer
       if: contains(inputs.profile, 'singularity')
-      uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2
+      uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
 
     - name: Set up Singularity
       if: contains(inputs.profile, 'singularity')

nf_core/pipeline-template/.github/workflows/pr-comment.yml

@@ -60,7 +60,7 @@ jobs:
 
       - name: Post PR comment
         if: steps.meta.outputs.post == 'true'
-        uses: marocchino/sticky-pull-request-comment@70d2764d1a7d5d9560b100cbea0077fc8f633987 # v3
+        uses: marocchino/sticky-pull-request-comment@5770ad5eb8f42dd2c4f34da00c94c5381e49af88 # v3.0.5
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.meta.outputs.pr_number }}

nf_core/pipeline-template/.github/workflows/release-announcements.yml

@@ -18,7 +18,7 @@ jobs:
         id: get_description
         run: |
           echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT
-      - uses: rzr/fediverse-action@563159eb8d45f70ab6aaba36ed55cd037e51f441 # master
+      - uses: rzr/fediverse-action@66c2cbb5b1997666b0e28d597631b6a4f09a2719 # v0.0.6
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
           host: "mstdn.science" # custom host if not "mastodon.social" (default)