Move unit tests to deprecated

software/fastqc/test/deprecated/lib

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+../../../lib/

software/fastqc/test/deprecated/main.nf

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+#!/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/lib

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