Merge branch 'dev' into nf-core-template-merge-3.1.0

.github/workflows/awsfulltest.yml

@@ -45,9 +45,6 @@ jobs:
 
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

.github/workflows/ci.yml

@@ -1,10 +1,13 @@
-name: nf-core 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:
   push:
     branches:
-      - dev
+      - "dev"
   pull_request:
+    branches:
+      - "dev"
+      - "master"
   release:
     types: [published]
   workflow_dispatch:
@@ -13,18 +16,34 @@ env:
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+  NFTEST_VER: "0.9.0"
 
 concurrency:
-  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
 jobs:
+  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", "23.10.0"]' | tee -a $GITHUB_OUTPUT
+          fi
+
   test:
     name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/funcscan') }}"
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
         NXF_VER:
           - "24.04.2"
@@ -35,6 +54,17 @@ jobs:
           - "singularity"
         test_name:
           - "test"
+          - "test_nothing"
+          - "test_bakta"
+          - "test_prokka"
+          - "test_bgc_pyrodigal"
+          - "test_bgc_bakta"
+          - "test_bgc_prokka"
+          - "test_taxonomy_pyrodigal"
+          - "test_taxonomy_bakta"
+          - "test_taxonomy_prokka"
+          - "test_preannotated"
+          - "test_preannotated_bgc"
         isMaster:
           - ${{ github.base_ref == 'master' }}
         # Exclude conda and singularity on dev
@@ -52,6 +82,14 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - name: Check out test data
+        uses: actions/checkout@v3
+        with:
+          repository: nf-core/test-datasets
+          ref: funcscan
+          path: test-datasets/
+          fetch-depth: 1
+
       - name: Set up Apptainer
         if: matrix.profile == 'singularity'
         uses: eWaterCycle/setup-apptainer@main
@@ -80,6 +118,23 @@ jobs:
       - name: Clean up Disk space
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
+      - name: Install nf-test
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
+          sudo mv nf-test /usr/local/bin/
+
       - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
+          nf-test test --tag ${{ matrix.test_name }} --profile ${{ matrix.test_name }},${{ matrix.profile }} --junitxml=test.xml
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/*/tests/output/pipeline_info/software_versions.yml
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: "*.xml"

.gitignore

@@ -7,3 +7,4 @@ testing/
 testing*
 *.pyc
 null/
+.nf-test*

.nf-core.yml

@@ -3,12 +3,14 @@ lint:
 nf_core_version: 3.1.0
 repository_type: pipeline
 template:
-  author: Jasmin Frangenberg, Anan Ibrahim, Louisa Perelo, Moritz E. Beber, James
-    A. Fellows Yates
+  author: Jasmin Frangenberg, Anan Ibrahim, Louisa Perelo, Moritz E. Beber, James A. Fellows Yates
   description: Pipeline for screening for functional components of assembled contigs
   force: false
   is_nfcore: true
   name: funcscan
   org: nf-core
   outdir: .
+  skip_features:
+    - igenomes
+    - fastqc
   version: 2.1.0dev

.prettierignore

@@ -10,3 +10,4 @@ testing/
 testing*
 *.pyc
 bin/
+tests/