Convert ngscheckmate/fastq to nf-test

modules/nf-core/ngscheckmate/fastq/tests/main.nf.test

@@ -0,0 +1,130 @@
+nextflow_process {
+
+    name "Test Process NGSCHECKMATE_FASTQ"
+    script "../main.nf"
+    process "NGSCHECKMATE_FASTQ"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "ngscheckmate"
+    tag "ngscheckmate/fastq"
+    tag "ngscheckmate/patterngenerator"
+    tag "gawk"
+    tag "bedtools/makewindows"
+    tag "bowtie/build"
+
+    setup {
+
+        run("GAWK" , alias: "GAWK_FAI") {
+            script "../../../gawk/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id: 'sarscov2' ],
+                    file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+                    ]
+                input[1] = []
+                """
+            }
+        }
+
+        run("BEDTOOLS_MAKEWINDOWS") {
+            script "../../../bedtools/makewindows/main.nf"
+            process {
+                """
+                input[0] = GAWK_FAI.out.output
+                """
+            }
+        }
+
+        run("GAWK" , alias: "GAWK_BED") {
+            script "../../../gawk/main.nf"
+            process {
+                """
+                input[0] = BEDTOOLS_MAKEWINDOWS.out.bed
+                input[1] = []
+                """
+            }
+        }
+
+        run("BOWTIE_BUILD") {
+            script "../../../bowtie/build/main.nf"
+            process {
+                """
+                input[0] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                """
+            }
+        }
+
+        run("NGSCHECKMATE_PATTERNGENERATOR") {
+            script "../../patterngenerator/main.nf"
+            process {
+                """
+                input[0] = GAWK_BED.out.output
+                input[1] = [
+                    [ id: 'sarscov2' ],
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                ]
+                input[2] = BOWTIE_BUILD.out.index
+                """
+            }
+        }
+
+    }
+
+    test("sarscov2 - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_paired', single_end:false ], // meta map
+                    [
+                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+                    ]
+                ]
+                input[1] = NGSCHECKMATE_PATTERNGENERATOR.out.pt
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_paired', single_end:false ], // meta map
+                    [
+                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+                    ]
+                ]
+                input[1] = NGSCHECKMATE_PATTERNGENERATOR.out.pt
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/ngscheckmate/fastq/tests/main.nf.test.snap

@@ -0,0 +1,72 @@
+{
+    "sarscov2 - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_paired",
+                            "single_end": false
+                        },
+                        "test_paired.vaf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,9a5d7a8d9148b2ca1ad7d53764ca511a"
+                ],
+                "vaf": [
+                    [
+                        {
+                            "id": "test_paired",
+                            "single_end": false
+                        },
+                        "test_paired.vaf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9a5d7a8d9148b2ca1ad7d53764ca511a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.1"
+        },
+        "timestamp": "2024-05-23T08:52:38.804007828"
+    },
+    "sarscov2 - bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_paired",
+                            "single_end": false
+                        },
+                        "test_paired.vaf:md5,a2d18480c8bb7045c39c063faef7e1e4"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,9a5d7a8d9148b2ca1ad7d53764ca511a"
+                ],
+                "vaf": [
+                    [
+                        {
+                            "id": "test_paired",
+                            "single_end": false
+                        },
+                        "test_paired.vaf:md5,a2d18480c8bb7045c39c063faef7e1e4"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9a5d7a8d9148b2ca1ad7d53764ca511a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.1"
+        },
+        "timestamp": "2024-05-23T08:52:22.506102602"
+    }
+}

tests/modules/nf-core/ngscheckmate/fastq/nextflow.config → modules/nf-core/ngscheckmate/fastq/tests/nextflow.config

@@ -1,22 +1,16 @@
 process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
     withName: BEDTOOLS_MAKEWINDOWS {
         ext.args = '-w 1'
         ext.prefix = 'test_split'
     }
-
     withName: GAWK_BED {
         ext.args2 = '\'NR > 20 && NR < 20000 && FS = OFS = "\t" { print $0 FS "rs1" FS "G" FS "C" }\''
         ext.prefix = 'snp'
         ext.suffix = "bed"
     }
-
     withName: GAWK_FAI {
         ext.args2 = '\'BEGIN { FS = OFS = "\t" } { print \$1 FS "0" FS \$2 }\''
         ext.prefix = 'fasta'
         ext.suffix = "bed"
     }
-
 }

modules/nf-core/ngscheckmate/fastq/tests/tags.yml

@@ -0,0 +1,2 @@
+ngscheckmate/fastq:
+  - "modules/nf-core/ngscheckmate/fastq/**"

tests/config/pytest_modules.yml

@@ -1199,9 +1199,6 @@ ngmaster:
 ngmerge:
   - modules/nf-core/ngmerge/**
   - tests/modules/nf-core/ngmerge/**
-ngscheckmate/fastq:
-  - modules/nf-core/ngscheckmate/fastq/**
-  - tests/modules/nf-core/ngscheckmate/fastq/**
 ngscheckmate/patterngenerator:
   - modules/nf-core/ngscheckmate/patterngenerator/**
   - tests/modules/nf-core/ngscheckmate/patterngenerator/**