Update ci

Author: JoseEspinosa

.github/workflows/ci.yml

@@ -33,13 +33,8 @@ jobs:
           - "conda"
           - "docker"
           - "singularity"
-        parameters:
-          - ""
-          - "--skip_trimming"
-          - "--skip_consensus_peaks"
-          - "--aligner bowtie2"
-          - "--aligner chromap"
-          - "--aligner star"
+        test_name:
+          - "test"
         isMaster:
           - ${{ github.base_ref == 'master' }}
         # Exclude conda and singularity on dev
@@ -87,8 +82,58 @@ jobs:
       - name: Clean up Disk space
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.parameters }} | ${{ matrix.profile }}"
+      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,${{ matrix.profile }} --outdir ./results ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+
+      - name: Run pipeline with test data (singularity)
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results
+        if: "${{ github.base_ref == 'master' }}"
+
+      - name: Run pipeline with test data (conda)
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results
+        if: "${{ github.base_ref == 'master' }}"
+
+  parameters:
+    name: Test workflow parameters
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/chipseq') }}"
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        NXF_VER:
+          - "24.04.2"
+          - "latest-everything"
+        parameters:
+          - "--skip_trimming"
+          - "--skip_consensus_peaks"
+          - "--aligner bowtie2"
+          - "--aligner chromap"
+          - "--aligner star"
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v2
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - name: Run pipeline with various parameters (docker)
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
+
+      - name: Run pipeline with various parameters (singularity)
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results ${{ matrix.parameters }}
+        if: "${{ github.base_ref == 'master' }}"
+
+      - name: Run pipeline with various parameters (conda)
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results ${{ matrix.parameters }}
         if: "${{ github.base_ref == 'master' }}"