Adapt script for meta

software/fastqc/test/main.nf

@@ -1,73 +1,35 @@
 #!/usr/bin/env nextflow
-import checksum
-nextflow.preview.dsl = 2
 
-params.out_dir = "test_output"
+nextflow.enable.dsl = 2
-params.fastqc_args = ''
+
+params.outdir = "results/"
 params.publish_dir_mode = "copy"
+params.conda = false
 
 include { FASTQC } from '../main.nf'
 
-/**
+/*
- * Test if FASTQC runs with single-end data
+ * Test 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
+    def reads = []
-    FASTQC.out.html.map { name, is_single_end, html_file ->
+    reads = [ [ id:'test', single_end:true ],
-        html_hash = checksum.getMD5(new File("${html_file}"));
+              [ file('input/test_single_end.fastq.gz', checkIfExists: true) ] ]
 
-        assert name == "test_single_end"
+    FASTQC ( reads, [:] )
-        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
+ * Test 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
+    def reads = []
-    FASTQC.out.html.map { name, is_single_end, html_files ->
+    reads = [ [ id:'test', single_end:false ],
-        html_r1 = html_files[0]
+              [ file('input/test_R1.fastq.gz', checkIfExists: true), file('input/test_R2.fastq.gz', checkIfExists: true) ] ]
-        html_r2 = html_files[1]
 
-        html_r1_hash = checksum.getMD5(new File("${html_r1}"));
+    FASTQC ( reads, [:] )
-        html_r2_hash = checksum.getMD5(new File("${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 {