added nf-test files for art/illumina (#4038)

* added nf-test files

- two tests (single- and paired-end)
- including two nextflow.configs for `ext.args`

* change tests topass on conda/mamba and singularity/docker

- due to gzip the fastq files will have different md5sums with different engines

* added art/illumina

- should trigger the nf-test CI

* extended tag to art/illumina

* fixed typos -.-

* fixed typo again

- missing quote

* renamed test.yml to tags.yml

* removed art/illumina

* added <tool> tag

* added nf-tests for -stub-run

---------

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

modules/nf-core/art/illumina/tests/main.nf.test

@@ -0,0 +1,181 @@
+nextflow_process {
+
+    name "Test Process ART_ILLUMINA"
+    script "../main.nf"
+    process "ART_ILLUMINA"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "art"
+    tag "art/illumina"
+
+    test("single-end") {
+
+        config "./single-end.nextflow.config"
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [id: 'test'],
+                    [
+                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                ]
+                input[1] = 'HS25'
+                input[2] = '15'
+                input[3] = '150'
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert path(process.out.aln.get(0).get(1)).md5 == "7aa88720911ca1a862e4a24d57435e3c"},
+                { assert path(process.out.fastq.get(0).get(1)).linesGzip.size() == 11880 },
+                {
+                    def read_name = path(process.out.fastq.get(0).get(1)).linesGzip[0]
+                    assert read_name.equals("@MT192765.1-2970")
+                },
+                {
+                    def read = path(process.out.fastq.get(0).get(1)).linesGzip[1]
+                    assert read.equals("GAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCTATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGC")
+                },
+                {
+                    def read_qc = path(process.out.fastq.get(0).get(1)).linesGzip[3]
+                    assert read_qc.equals("C1CGGGCGG=GGGJGJG=JJCJJJCJGJJJJGJJJ1JJJGJJGGJGJJGGGJJGJJJCJGGGJ(=G1GGG(CCCGGGCGCGGGCCGCCG8GGGGGGGGGGCC(CGG1GGGG1GGCGCGGCGGGCGCGGGCGGGGCGCCGGGGGCG8GGGG")
+                },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+
+    }
+
+        test("single-end-stub") {
+
+        options "-stub-run"
+        config "./single-end.nextflow.config"
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [id: 'test'],
+                    [
+                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                ]
+                input[1] = 'HS25'
+                input[2] = '15'
+                input[3] = '150'
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("paired-end") {
+
+        config "./paired-end.nextflow.config"
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [id: 'test'],
+                    [
+                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                ]
+                input[1] = 'HS25'
+                input[2] = '15'
+                input[3] = '150'
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert path(process.out.fastq.get(0).get(1).get(0)).linesGzip.size() == 5940 },
+                                {
+                    def read_name = path(process.out.fastq.get(0).get(1).get(0)).linesGzip[0]
+                    assert read_name.equals("@MT192765.1-2970/1")
+                },
+                {
+                    def read = path(process.out.fastq.get(0).get(1).get(0)).linesGzip[1]
+                    assert read.equals("GTTGCGACTACGTGATGAGGAACGAGAAGCGGCTTGACTGCCGCCTCTGCTCCCTTCTGCGTAGAAGCCTTTTGGCAATGTTGTTCCTTGAGGAAGTTGTAGCACGATTGCAGCATTGTTAGCAGGATTGCGGGTGCCAATGTGATCTTT")
+                },
+                {
+                    def read_qc = path(process.out.fastq.get(0).get(1).get(0)).linesGzip[3]
+                    assert read_qc.equals("CCCGGGGGGGGGGGCJCJJJJJ1JJJGJJ(JJJGGGJJJJGGJGJJGJJJCCGCJCJC=GCGGG8GJGGGCGG=1G1CJGG=GGCGGCGGGGGCCGG=8GJCCGCCGCGGGGGGGC=GGG=CCGCGGCGGGCC=GGGGGGCGGCCCGCGG")
+                },
+                { assert path(process.out.fastq.get(0).get(1).get(1)).linesGzip.size() == 5940 },
+                {
+                    def read_name = path(process.out.fastq.get(0).get(1).get(1)).linesGzip[0]
+                    assert read_name.equals("@MT192765.1-2970/2")
+                },
+                {
+                    def read = path(process.out.fastq.get(0).get(1).get(1)).linesGzip[1]
+                    assert read.equals("GAGCTACCAGACGAATTCGTGGTGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCTGGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCT")
+                },
+                {
+                    def read_qc = path(process.out.fastq.get(0).get(1).get(1)).linesGzip[3]
+                    assert read_qc.equals("1CCGGGGGGGCGGGJJJJJGJG1GJGJ=JGJJCJJJCJJJGJ1GJGJGGJJC8JGG=JGGCGCCGCGGCCCGJCGGGGCJC==CGG88CGGGCGGGCCCGGC8JJJJCGGCGGCCGGGG=CGGGGCCGGCCCGCGCCCCG8GGGG=GGGC")
+                },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+
+    }
+
+    test("paired-end-stub") {
+
+        options "-stub-run"
+        config "./paired-end.nextflow.config"
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [id: 'test'],
+                    [
+                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                ]
+                input[1] = 'HS25'
+                input[2] = '15'
+                input[3] = '150'
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/art/illumina/tests/paired-end.nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    ext.args = '-p -m 250 -s 50 -rs 42'
+
+}

modules/nf-core/art/illumina/tests/single-end.nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    ext.args = '-rs 42'
+
+}

modules/nf-core/art/illumina/tests/tags.yml

@@ -0,0 +1,2 @@
+art/illumina:
+  - modules/nf-core/art/illumina/**

tests/config/pytest_modules.yml

@@ -114,10 +114,6 @@ arriba:
   - modules/nf-core/arriba/**
   - tests/modules/nf-core/arriba/**
 
-art/illumina:
-  - modules/nf-core/art/illumina/**
-  - tests/modules/nf-core/art/illumina/**
-
 artic/guppyplex:
   - modules/nf-core/artic/guppyplex/**
   - tests/modules/nf-core/artic/guppyplex/**