Merge pull request #22 from seqeralabs/update_ci

Copy in CI from fetchngs

.github/include.yaml

@@ -0,0 +1,10 @@
+".":
+  - ./.github/workflows/**
+  - ./nf-test.config
+  - ./nextflow.config
+tests:
+  - ./assets/*
+  - ./bin/*
+  - ./conf/*
+  - ./main.nf
+  - ./nextflow_schema.json

.github/workflows/ci.yml

@@ -1,76 +1,92 @@
-name: nf-aggregate CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+name: nf-core CI
 on:
   pull_request:
   release:
-    types:
-      - published
+    types: [published]
   merge_group:
     types:
       - checks_requested
     branches:
       - master
+      - dev
 
 env:
   NXF_ANSI_LOG: false
+  NFT_VER: "0.8.4"
+  NFT_WORKDIR: "~"
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
+  TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }}
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 
 jobs:
   changes:
-    name: Find tags to test
+    name: Check for changes
     runs-on: ubuntu-latest
     outputs:
-      tags: ${{ steps.get_tags.outputs.result }}
+      nf_test_files: ${{ steps.list.outputs.components }}
     steps:
       - 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
-      - name: Get tags using yq
-        id: get_tags
-        uses: mikefarah/yq@master
         with:
-          cmd: yq -e '. | keys | tojson' .github/tags.yml
+          fetch-depth: 0
+
+      - name: List nf-test files
+        id: list
+        uses: adamrtalbot/[email protected]
+        with:
+          head: ${{ github.sha }}
+          base: origin/${{ github.base_ref }}
+          include: .github/include.yaml
 
-  nf-test:
-    name: nf-test ${{ matrix.tags }} ${{ matrix.profile }} nf-${{ matrix.NXF_VER }}
+      - name: print list of nf-test files
+        run: |
+          echo ${{ steps.list.outputs.components }}
+
+  test:
+    name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
     needs: [changes]
-    if: needs.changes.outputs.tags != '[]'
+    if: needs.changes.outputs.nf_test_files != '[]'
     runs-on: ubuntu-latest
-    env:
-      TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }}
     strategy:
       fail-fast: false
       matrix:
         NXF_VER:
-          - "23.10.0"
           - "latest-everything"
-        tags: ${{ fromJson(needs.changes.outputs.tags) }}
+        nf_test_files: ["${{ fromJson(needs.changes.outputs.nf_test_files) }}"]
         profile:
           - "docker"
 
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          architecture: "x64"
+
+      - name: Install pdiff to see diff between nf-test snapshots
+        run: |
+          python -m pip install --upgrade pip
+          pip install pdiff
+
       - 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.NFTEST_VER }}-nftest
+          key: ${{ runner.os }}-${{ env.NFT_VER }}-nftest
 
       - name: Install nf-test
         if: steps.cache-software.outputs.cache-hit != 'true'
@@ -80,7 +96,12 @@ jobs:
 
       - name: Run nf-test
         run: |
-          nf-test test --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml --verbose
+          nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
+
+      - uses: pcolby/tap-summary@v1
+        with:
+          path: >-
+            test.tap
 
       - name: Output log on failure
         if: failure()
@@ -96,11 +117,13 @@ jobs:
 
   confirm-pass:
     runs-on: ubuntu-latest
-    needs: [changes, nf-test]
+    needs:
+      - changes
+      - test
     if: always()
     steps:
       - name: All tests ok
-        if: ${{ success() || !contains(needs.*.result, 'failure') }}
+        if: ${{ !contains(needs.*.result, 'failure') }}
         run: exit 0
       - name: One or more tests failed
         if: ${{ contains(needs.*.result, 'failure') }}

nf-test.config

@@ -9,5 +9,5 @@ config {
     configFile "tests/nextflow.config"
 
     // run all test with the defined docker profile from the main nextflow.config
-    profile ""
+    profile "test"
 }