Merge pull request #80 from nf-core/pytest-workflow

Pytest-workflow
nf-core · Nov 24, 2020 · 794a5cb · 794a5cb
2 parents 751204e + 83539fc
commit 794a5cb
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diff --git a/.github/workflows/fastqc.yml b/.github/workflows/fastqc.yml
@@ -26,5 +26,12 @@ jobs:
         wget -qO- get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin/
 
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.x"
+    - name: Install dependencies
+      run: python -m pip install --upgrade pip pytest-workflow
+
     # Test the module
-    - run: nextflow run ./software/fastqc/test/ -profile docker
+    - run: pytest --tag fastqc --symlink --wt 2
diff --git a/software/fastqc/test/deprecated/lib b/software/fastqc/test/deprecated/lib
diff --git a/software/fastqc/test/deprecated/main.nf b/software/fastqc/test/deprecated/main.nf
diff --git a/software/fastqc/test/input/test_R1.fastq.gz b/software/fastqc/test/input/test_R1.fastq.gz
diff --git a/software/fastqc/test/input/test_R2.fastq.gz b/software/fastqc/test/input/test_R2.fastq.gz
diff --git a/software/fastqc/test/input/test_single_end.fastq.gz b/software/fastqc/test/input/test_single_end.fastq.gz
diff --git a/software/fastqc/test/main.nf b/software/fastqc/test/main.nf
diff --git a/software/fastqc/test/output/test_paired_end/test_1_fastqc.html b/software/fastqc/test/output/test_paired_end/test_1_fastqc.html
diff --git a/software/fastqc/test/output/test_paired_end/test_1_fastqc.zip b/software/fastqc/test/output/test_paired_end/test_1_fastqc.zip
diff --git a/software/fastqc/test/output/test_paired_end/test_2_fastqc.html b/software/fastqc/test/output/test_paired_end/test_2_fastqc.html
diff --git a/software/fastqc/test/output/test_paired_end/test_2_fastqc.zip b/software/fastqc/test/output/test_paired_end/test_2_fastqc.zip
diff --git a/software/fastqc/test/output/test_single_end/test_fastqc.html b/software/fastqc/test/output/test_single_end/test_fastqc.html
diff --git a/software/fastqc/test/output/test_single_end/test_fastqc.zip b/software/fastqc/test/output/test_single_end/test_fastqc.zip
diff --git a/software/fastqc/test/nextflow.config → tests/config/nextflow.config b/software/fastqc/test/nextflow.config → tests/config/nextflow.config
diff --git a/tests/software/fastqc/main.nf b/tests/software/fastqc/main.nf
@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTQC as FASTQC_SE } from '../../../software/fastqc/main.nf'  addParams( options: [ publish_dir:'test_single_end' ] )
+include { FASTQC as FASTQC_PE } from '../../../software/fastqc/main.nf'  addParams( options: [ publish_dir:'test_paired_end' ] )
+
+/*
+ * Test with single-end data
+ */
+workflow test_single_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
+
+    FASTQC_SE ( input )
+}
+
+/*
+ * Test with paired-end data
+ */
+workflow test_paired_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
+
+    FASTQC_PE ( input )
+}
diff --git a/tests/software/fastqc/test.yml b/tests/software/fastqc/test.yml
@@ -0,0 +1,20 @@
+- name: Run fastqc single-end test workflow
+  command: nextflow run ./tests/software/fastqc/ -profile docker -entry test_single_end -c tests/config/nextflow.config
+  tags:
+    - fastqc
+  files:
+    - path: output/test_single_end/test_fastqc.html
+      md5sum: 7027e72c3e55292c1567f12e02565e3b
+    - path: output/test_single_end/test_fastqc.zip
+
+- name: Run fastqc paired-end test workflow
+  command: nextflow run ./tests/software/fastqc/ -profile docker -entry test_paired_end -c tests/config/nextflow.config
+  tags:
+    - fastqc
+  files:
+    - path: output/test_paired_end/test_1_fastqc.html
+      md5sum: b3796b4323dc34970b7461f813135254
+    - path: output/test_paired_end/test_2_fastqc.html
+      md5sum: 55182467f48ca5ed88a2608ea57a1afc
+    - path: output/test_paired_end/test_1_fastqc.zip
+    - path: output/test_paired_end/test_2_fastqc.zip