Revert changes in ci.yml and linting.yml

.github/workflows/ci.yml

@@ -11,7 +11,6 @@ on:
       - master
   release:
     types: [published]
-  workflow_dispatch:
 
 env:
   NXF_ANSI_LOG: false
@@ -37,7 +36,7 @@ jobs:
         NXF_VER:
           - "24.04.2"
           - "latest-everything"
-        profile: ["docker"] # TODO should we add singularity and conda to the profiles?
+        profile: ["docker"]
     env:
       SHARDS: "4"
     steps:
@@ -64,21 +63,19 @@ jobs:
         with:
           version: ${{ env.NFT_VER }}
 
-      - name: Run pipeline with test data (docker)
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
+      - name: Run Tests (Shard ${{ matrix.shard }}/${{ env.SHARDS }})
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          nf-test test \
+              --ci \
+              --shard ${{ matrix.shard }}/${{ env.SHARDS }} \
+              --changed-since HEAD^ \
+              --profile "+${{ matrix.profile }}" \
+              --filter pipeline \
+              --junitxml=test.xml
 
-      - name: Run pipeline with test data (singularity)
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results
-        if: "${{ github.base_ref == 'master' }}"
-
-      - name: Run pipeline with test data (conda)
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results
-        if: "${{ github.base_ref == 'master' }}"
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: test.xml
+          annotate_only: true

.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 pipelines lint` and markdown lint tests to ensure
+# It runs the `nf-core lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
 on:
   push:
@@ -41,32 +41,17 @@ jobs:
           python-version: "3.12"
           architecture: "x64"
 
-      - name: read .nf-core.yml
-        uses: pietrobolcato/[email protected]
-        id: read_yml
-        with:
-          config: ${{ github.workspace }}/.nf-core.yaml
-
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
-
-      - 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
+          pip install nf-core
 
-      - name: Run nf-core pipelines lint --release
-        if: ${{ github.base_ref == 'master' }}
+      - name: Run nf-core lint
         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
+        run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Save PR number
         if: ${{ always() }}