Tidy up CI workflow a bit

.github/workflows/ci.yml

@@ -40,14 +40,13 @@ jobs:
           - "--save_align_intermeds --save_reference"
           - "--featurecounts_group_type false"
           - "--trimmer fastp"
+
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+      - name: Setup Nextflow
+        uses: nf-core/[email protected]
 
       - name: Run pipeline with STAR and various parameters
         run: |
@@ -64,12 +63,10 @@ jobs:
           - "--rsem_index false"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+      - name: Setup Nextflow
+        uses: nf-core/[email protected]
 
       - name: Run pipeline with RSEM STAR and various parameters
         run: |
@@ -86,12 +83,10 @@ jobs:
           - "--hisat2_index false"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+      - name: Setup Nextflow
+        uses: nf-core/[email protected]
 
       - name: Run pipeline with HISAT2 and various parameters
         run: |
@@ -112,12 +107,10 @@ jobs:
           - "--pseudo_aligner kallisto --kallisto_index false --transcript_fasta false"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+      - name: Setup Nextflow
+        uses: nf-core/[email protected]
 
       - name: Run pipeline with Salmon or Kallisto and various parameters
         run: |
@@ -135,7 +128,7 @@ jobs:
           python-version: "3.11"
           architecture: "x64"
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -169,7 +162,7 @@ jobs:
             pyproject.toml
             tower.yml
 
-      - name: debug
+      - name: print-changed-dirs
         run: |
           echo ${{ steps.changed_files.outputs.any_modified }}
           echo ${{ steps.changed_files.outputs.all_changed_files }}
@@ -185,11 +178,11 @@ jobs:
             -p ${{ steps.changed_files.outputs.all_changed_files }} ${{ steps.changed_files.outputs.changed_keys }} \
           ) >> $GITHUB_OUTPUT
 
-      - name: debug2
+      - name: print-test-tags
         run: |
           echo ${{ steps.list.outputs.tags }}
 
-  nf-test:
+  test:
     name: ${{ matrix.tags }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
     needs: [nf-test-changes]
     if: needs.nf-test-changes.outputs.changes
@@ -199,17 +192,17 @@ jobs:
       matrix:
         NXF_VER:
           - "latest-everything"
-          - "23.04"
+          - "23.04.0"
         tags: ["${{ fromJson(needs.nf-test-changes.outputs.tags) }}"]
         profile:
           - "docker"
 
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@v4
 
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v1.5
         with:
           version: "${{ matrix.NXF_VER }}"
 
@@ -261,7 +254,7 @@ jobs:
 
   confirm-pass:
     runs-on: ubuntu-latest
-    needs: [nf-test, star_salmon, star_rsem, hisat2, pseudo]
+    needs: [test, star_salmon, star_rsem, hisat2, pseudo]
     if: always()
     steps:
       - name: All tests ok