Merge pull request #341 from nf-core/fromSamplesheet

Use fromSamplesheet

.github/workflows/ci.yml

@@ -21,58 +21,59 @@ concurrency:
   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", "23.04.0"]' | tee -a $GITHUB_OUTPUT
+          fi
+
   test:
     name: Run pipeline with test data
+    needs: define_nxf_versions
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
-        aligner:
+        NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
+        test_tags:
           - "bismark"
           - "bismark_hisat"
           - "bwameth"
         profile:
           - "docker"
-    steps:
-      # Skip if it's a pull_request to dev and NXF_VER is '22.10.1'
-      - name: Skip condition
-        id: condition
-        run: |
-          if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
-            echo "skip=true" >> $GITHUB_OUTPUT
-          fi
 
+    steps:
       - name: Check out pipeline code
-        if: steps.condition.outputs.skip != 'true'
         uses: actions/checkout@v3
 
       - name: Hash Github Workspace
-        if: steps.condition.outputs.skip != 'true'
         id: hash_workspace
         run: |
           echo "digest=$(echo methylseq2_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
 
       - name: Cache test data
-        if: steps.condition.outputs.skip != 'true'
         id: cache-testdata
         uses: actions/cache@v3
         with:
           path: test-datasets/
           key: ${{ steps.hash_workspace.outputs.digest }}
 
       - name: Check out test data
-        if: steps.cache-testdata.outputs.cache-hit != 'true' && steps.condition.outputs.skip != 'true'
         uses: actions/checkout@v3
         with:
           repository: nf-core/test-datasets
           ref: methylseq
           path: test-datasets/
 
       - name: Replace remote paths in samplesheets
-        if: steps.condition.outputs.skip != 'true'
         run: |
           for f in ./test-datasets/samplesheet/*csv; do
             sed -i 's=https://github.com/nf-core/test-datasets/raw/methylseq/=./test-datasets/=g' $f
@@ -83,25 +84,27 @@ jobs:
           done;
 
       - name: Install Nextflow
-        if: steps.condition.outputs.skip != 'true'
         uses: nf-core/setup-nextflow@v1
         with:
           version: "${{ matrix.NXF_VER }}"
 
       - name: Install nf-test
-        if: steps.condition.outputs.skip != 'true'
         run: |
           wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
           sudo mv nf-test /usr/local/bin/
 
       - name: Run nf-test
-        if: steps.condition.outputs.skip != 'true'
         run: |
-          nf-test test tests/pipeline/${{ matrix.aligner }}/ --profile "test,${{ matrix.profile }}" --tap=test.tap
+          nf-test test --tag ${{ matrix.test_tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml
 
-      # If the test fails, output the software_versions.yml using the 'batcat' utility
       - 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: test.xml

CHANGELOG.md

@@ -7,6 +7,7 @@
 - Updated template to nf-core/tools v2.9
 - Updated nf-core modules for FastQC, samtools sort, samtools flagstat
   - Removes problematic `-m` memory assignment for samtools sort [#81](https://github.com/nf-core/methylseq/issues/81)
+- Use `fromSamplesheet` from nf-validation [#341](https://github.com/nf-core/methylseq/pull/341)
 
 ### Bug fixes & refactoring
 

assets/schema_input.json

@@ -10,15 +10,21 @@
             "sample": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces"
+                "errorMessage": "Sample name must be provided and cannot contain spaces",
+                "meta": ["id"]
             },
             "fastq_1": {
                 "type": "string",
+                "format": "file-path",
+                "exists": true,
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             },
             "fastq_2": {
                 "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
+                "type": "string",
+                "format": "file-path",
+                "exists": true,
                 "anyOf": [
                     {
                         "type": "string",