Merge pull request #197 from nf-core/nf-validation

Add nf-validation

.github/workflows/ci.yml

@@ -73,9 +73,7 @@ jobs:
           architecture: "x64"
 
       - name: Install pdiff to see diff between nf-test snapshots
-        run: |
-          python -m pip install --upgrade pip
-          pip install pdiff
+        run: python -m pip install --upgrade pip pdiff cryptography
 
       - uses: nf-core/setup-nf-test@v1
 
@@ -84,6 +82,9 @@ jobs:
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
 
       - name: Run nf-test
+        env:
+          NFT_DIFF: "pdiff"
+          NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
         run: |
           nf-test test --verbose --tag PIPELINE --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
 

assets/samplesheet.csv

@@ -1,2 +1,2 @@
 sample,fastq_1,fastq_2
-SRR4292758,https://github.com/nf-core/test-datasets/raw/hic/data/SRR4292758_00_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/hic/data/SRR4292758_00_R2.fastq.gz
+SRR4292758,https://raw.githubusercontent.com/nf-core/test-datasets/hic/data/SRR4292758_00_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/hic/data/SRR4292758_00_R2.fastq.gz

assets/schema_input.json

@@ -28,6 +28,6 @@
                 "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             }
         },
-        "required": ["sample", "fastq_1"]
+        "required": ["sample", "fastq_1", "fastq_2"]
     }
 }