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

Pytest-workflow

.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

software/fastqc/test/deprecated/lib

@@ -1 +0,0 @@
-../../../lib/

software/fastqc/test/deprecated/main.nf

@@ -1,76 +0,0 @@
-#!/usr/bin/env nextflow
-import checksum
-nextflow.preview.dsl = 2
-
-params.out_dir = "test_output"
-params.fastqc_args = ''
-params.publish_dir_mode = "copy"
-
-include { FASTQC } from '../main.nf'
-
-/**
- * Test if FASTQC runs with single-end data
- */
-workflow test_single_end {
-    input_files = Channel.fromPath("${baseDir}/input/test_single_end.fastq.gz")
-                    .map {f -> [f.name.replace(".fastq.gz", ""), true, f]}
-    FASTQC(input_files)
-
-    // test that the output looks as expected
-    FASTQC.out.html.map { name, is_single_end, html_file ->
-        html_hash = checksum.getMD5(new File("${html_file}"));
-
-        assert name == "test_single_end"
-        assert is_single_end == true
-        assert html_file.getName() == "test_single_end_fastqc.html"
-        // Hash seems to vary between local runs and GitHub Actions
-        // TODO: Might be solved when using Docker for tests?
-        // assert html_hash == "8ed68442ebb5b9706bf79b4f66701e15"
-    }
-    FASTQC.out.zip.map { name, is_single_end, zip_file ->
-        // NOTE: output zip files do not have a consistent hash
-        assert name == "test_single_end"
-        assert is_single_end == true
-        assert zip_file.getName() == "test_single_end_fastqc.zip"
-    }
-}
-
-/**
- * Test if FASTQC runs with paired end data
- */
-workflow test_paired_end {
-    input_files = Channel.fromFilePairs("input/test_R{1,2}.fastq.gz")
-                    .map {f -> [f[0], false, f[1]]}
-    FASTQC(input_files)
-
-    // test that the output looks as expected
-    FASTQC.out.html.map { name, is_single_end, html_files ->
-        html_r1 = html_files[0]
-        html_r2 = html_files[1]
-
-        html_r1_hash = checksum.getMD5(new File("${html_r1}"));
-        html_r2_hash = checksum.getMD5(new File("${html_r2}"));
-
-        assert name == "test_R"
-        assert is_single_end == false
-        assert html_r1.getName() == "test_R_1_fastqc.html"
-        assert html_r2.getName() == "test_R_2_fastqc.html"
-        assert html_r1_hash == "082c13ce7163ea0f52a66b83cb57b0f0"
-        assert html_r2_hash == "4ff04ec8da77e3af512f03b8c09a9e04"
-    }
-    FASTQC.out.zip.map { name, is_single_end, zip_files ->
-        zip_r1 = zip_files[0]
-        zip_r2 = zip_files[1]
-        // NOTE: output zip files do not have a consistent hash
-
-        assert name == "test_R"
-        assert is_single_end == false
-        assert zip_r1.getName() == "test_R_1_fastqc.zip"
-        assert zip_r2.getName() == "test_R_2_fastqc.zip"
-    }
-}
-
-workflow {
-    test_single_end()
-    test_paired_end()
-}

software/fastqc/test/input/test_R1.fastq.gz

@@ -1 +0,0 @@
-../../../../tests/data/fastq/rna/test_R1.fastq.gz

software/fastqc/test/input/test_R2.fastq.gz

@@ -1 +0,0 @@
-../../../../tests/data/fastq/rna/test_R2.fastq.gz

software/fastqc/test/input/test_single_end.fastq.gz

@@ -1 +0,0 @@
-../../../../tests/data/fastq/rna/test_single_end.fastq.gz

software/fastqc/test/main.nf

@@ -1,36 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FASTQC as FASTQC_SE } from '../main.nf'  addParams( options: [ publish_dir:'test_single_end' ] )
-include { FASTQC as FASTQC_PE } from '../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("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
-
-    FASTQC_SE ( input )
-}
-
-/*
- * Test with paired-end data
- */
-workflow test_paired_end {
-
-    def input = []
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
-                file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
-
-    FASTQC_PE ( input )
-}
-
-workflow {
-    test_single_end()
-    test_paired_end()
-}

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 )
+}

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