refactor(pytest-workflow): Move fastqc tests to tests/

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_single_end.fastq.gz

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

software/fastqc/test/main.nf

@@ -1,31 +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 )
-}

tests/fastqc/input/test_single_end.fastq.gz

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

tests/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("${projectDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
+
+    FASTQC_SE ( input )
+}
+
+/*
+ * Test with paired-end data
+ */
+workflow test_paired_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
+                file("${projectDir}/../data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
+
+    FASTQC_PE ( input )
+}

tests/fastqc/nextflow.config

@@ -1,4 +1,3 @@
-
 params {
     outdir = "output/"
     publish_dir_mode = "copy"

tests/fastqc/test_fastqc.yml

@@ -1,5 +1,5 @@
 - name: Run fastqc single-end test workflow
-  command: nextflow run ./software/fastqc/test/ -profile docker -entry test_single_end
+  command: nextflow run ./tests/fastqc/ -profile docker -entry test_single_end
   tags:
     - fastqc
   files:
@@ -8,7 +8,7 @@
     - path: output/test_single_end/test_fastqc.zip
 
 - name: Run fastqc paired-end test workflow
-  command: nextflow run ./software/fastqc/test/ -profile docker -entry test_paired_end
+  command: nextflow run ./tests/fastqc/ -profile docker -entry test_paired_end
   tags:
     - fastqc
   files: