Replace tags strategy with implicit 'tags in test' strategy

.github/workflows/ci.yml

@@ -27,43 +27,101 @@ jobs:
     name: Check for changes
     runs-on: ubuntu-latest
     outputs:
-      # Expose matched filters as job 'tags' output variable
-      tags: ${{ steps.filter.outputs.changes }}
+      changes: ${{ steps.changed_files.outputs.any_modified }}
+      tags: ${{ steps.list.outputs.tags }}
     steps:
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+
+      - name: Cache nf-test installation
+        id: cache-software
+        uses: actions/cache@v3
+        with:
+          path: |
+            /usr/local/bin/nf-test
+            /home/runner/.nf-test/nf-test.jar
+          key: ${{ runner.os }}-${{ env.NFT_VER }}-nftest
+
+      - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
       - uses: actions/checkout@v3
-      - name: Combine all tags.yml files
-        id: get_username
-        run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml
-      - name: debug
-        run: cat .github/tags.yml
-      - uses: dorny/paths-filter@v2
-        id: filter
         with:
-          filters: ".github/tags.yml"
+          fetch-depth: 0
 
-  define_nxf_versions:
-    name: Choose nextflow versions to test against depending on target branch
-    runs-on: ubuntu-latest
-    outputs:
-      matrix: ${{ steps.nxf_versions.outputs.matrix }}
-    steps:
-      - id: nxf_versions
+      - uses: tj-actions/changed-files@v42
+        id: changed_files
+        with:
+          dir_names: "true"
+          output_renamed_files_as_deleted_and_added: "true"
+          # Define list of additional rules for testing paths
+          # Mostly, we define additional 'pipeline' or 'all' tests here
+          files_yaml: |
+            ".":
+              - .github/workflows/**
+              - nf-test.config
+              - nextflow.config
+            tests:
+              - assets/*
+              - bin/*
+              - conf/*
+              - main.nf
+              - nextflow_schema.json
+
+          files_ignore: |
+            .git*
+            .gitpod.yml
+            .prettierignore
+            .prettierrc.yml
+            **.md
+            **.png
+            modules.json
+            pyproject.toml
+            tower.yml
+
+      - name: debug
         run: |
-          if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
-            echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
-          else
-            echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT
-          fi
+          echo ${{ steps.changed_files.outputs.any_modified }}
+          echo ${{ steps.changed_files.outputs.all_changed_files }}
+          echo ${{ steps.changed_files.outputs.changed_keys }}
+
+      - name: nf-test list tags
+        id: list
+        if: ${{ steps.changed_files.outputs.any_modified }}
+        run: echo tags=$(nf-test list --silent --tags --format json ${{ steps.changed_files.outputs.all_changed_files }} ${{ steps.changed_files.outputs.changed_keys }}) >> $GITHUB_OUTPUT
+
+      - name: debug2
+        run: |
+          echo ${{ steps.list.outputs.tags }}
+
+  # define_nxf_versions:
+  #   name: Choose nextflow versions to test against depending on target branch
+  #   runs-on: ubuntu-latest
+  #   outputs:
+  #     matrix: ${{ steps.nxf_versions.outputs.matrix }}
+  #   steps:
+  #     - id: nxf_versions
+  #       run: |
+  #         if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
+  #           echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
+  #         else
+  #           echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT
+  #         fi
 
   test:
-    name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }}
-    needs: [changes, define_nxf_versions]
-    if: needs.changes.outputs.tags != '[]'
+    name: ${{ matrix.tags }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
+    needs: [changes]
+    if: needs.changes.outputs.changes
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
+        NXF_VER:
+          - "latest-everything"
+          - "23.04"
         tags: ["${{ fromJson(needs.changes.outputs.tags) }}"]
         profile:
           - "docker"
@@ -122,3 +180,21 @@ jobs:
         if: always() # always run even if the previous step fails
         with:
           report_paths: test.xml
+
+  confirm-pass:
+    runs-on: ubuntu-latest
+    needs: [test]
+    if: always()
+    steps:
+      - name: All tests ok
+        if: ${{ success() || !contains(needs.*.result, 'failure') }}
+        run: exit 0
+      - name: One or more tests failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
+
+      - name: debug-print
+        if: always()
+        run: |
+          echo "toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"

modules/local/multiqc_mappings_config/tests/main.nf.test

@@ -3,9 +3,8 @@ nextflow_process {
     name "Test process: MULTIQC_MAPPINGS_CONFIG"
     script "../main.nf"
     process "MULTIQC_MAPPINGS_CONFIG"
-    tag "modules"
-    tag "modules_local"
-    tag "multiqc_mappings_config"
+
+    tag "MULTIQC_MAPPINGS_CONFIG"
 
     test("Should run without failures") {
 

modules/local/sra_fastq_ftp/tests/main.nf.test

@@ -3,9 +3,8 @@ nextflow_process {
     name "Test process: SRA_FASTQ_FTP"
     script "../main.nf"
     process "SRA_FASTQ_FTP"
-    tag "modules"
-    tag "modules_local"
-    tag "sra_fastq_ftp"
+
+    tag "SRA_FASTQ_FTP"
 
     test("Should run without failures") {
 

modules/local/sra_ids_to_runinfo/tests/main.nf.test

@@ -3,9 +3,8 @@ nextflow_process {
     name "Test process: SRA_IDS_TO_RUNINFO"
     script "../main.nf"
     process "SRA_IDS_TO_RUNINFO"
-    tag "modules"
-    tag "modules_local"
-    tag "sra_ids_to_runinfo"
+
+    tag "SRA_IDS_TO_RUNINFO"
 
     test("Should run without failures") {
 

modules/local/sra_runinfo_to_ftp/tests/main.nf.test

@@ -3,9 +3,8 @@ nextflow_process {
     name "Test process: SRA_RUNINFO_TO_FTP"
     script "../main.nf"
     process "SRA_RUNINFO_TO_FTP"
-    tag "modules"
-    tag "modules_local"
-    tag "sra_runinfo_to_ftp"
+
+    tag "SRA_RUNINFO_TO_FTP"
 
     test("Should run without failures") {
 

modules/local/sra_to_samplesheet/tests/main.nf.test

@@ -3,9 +3,8 @@ nextflow_process {
     name "Test process: SRA_TO_SAMPLESHEET"
     script "../main.nf"
     process "SRA_TO_SAMPLESHEET"
-    tag "modules"
-    tag "modules_local"
-    tag "sra_to_samplesheet"
+
+    tag "SRA_TO_SAMPLESHEET"
 
     test("Should run without failures") {
 

subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test

@@ -3,9 +3,7 @@ nextflow_function {
 
     name "Test Functions"
     script "subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf"
-    tag 'subworkflows'
-    tag 'utils_nfcore_fetchngs_pipeline'
-    tag 'subworkflows/utils_nfcore_fetchngs_pipeline'
+    tag "UTILS_NFCORE_FETCHNGS_PIPELINE"
 
     test("Function isSraId") {
 

subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test

@@ -3,9 +3,7 @@ nextflow_workflow {
     name "Test Workflow PIPELINE_COMPLETION"
     script "subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf"
     workflow "PIPELINE_COMPLETION"
-    tag 'subworkflows'
-    tag 'utils_nfcore_fetchngs_pipeline'
-    tag 'subworkflows/utils_nfcore_fetchngs_pipeline'
+    tag "PIPELINE_COMPLETION"
 
     test("Should run") {
 

subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test

@@ -3,9 +3,7 @@ nextflow_workflow {
     name "Test Workflow PIPELINE_INITIALISATION"
     script "subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf"
     workflow "PIPELINE_INITIALISATION"
-    tag 'subworkflows'
-    tag 'utils_nfcore_fetchngs_pipeline'
-    tag 'subworkflows/utils_nfcore_fetchngs_pipeline'
+    tag 'PIPELINE_INITIALISATION'
 
     test("Should run") {