port gatk4/applyvqsr to nf-test (#5604)

* port to nf-test update stub

* add more assertions

* update snap

* update tbi test and snap

* change to check for filename

modules/nf-core/gatk4/applyvqsr/main.nf

@@ -52,7 +52,7 @@ process GATK4_APPLYVQSR {
     stub:
     prefix   = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.vcf.gz
+    echo "" | gzip > ${prefix}.vcf.gz
     touch ${prefix}.vcf.gz.tbi
 
     cat <<-END_VERSIONS > versions.yml

modules/nf-core/gatk4/applyvqsr/tests/allelspecificity.config

@@ -0,0 +1,5 @@
+process {
+    withName: GATK4_APPLYVQSR {
+        ext.args = '--mode SNP --truth-sensitivity-filter-level 99.0 -AS'
+    }
+}

modules/nf-core/gatk4/applyvqsr/tests/main.nf.test

@@ -0,0 +1,106 @@
+nextflow_process {
+
+    name "Test Process GATK4_APPLYVQSR"
+    script "../main.nf"
+    process "GATK4_APPLYVQSR"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/applyvqsr"
+
+    test("human - vcf") {
+
+        config "./no-allelspecificity.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches', checkIfExists: true)
+                        ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match("versions") },
+                { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") },
+                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match() }
+            )
+        }
+
+    }
+
+    test("human - vcf - allele-specific") {
+
+        config "./allelspecificity.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches', checkIfExists: true)
+                        ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match("versions_allelspecific") },
+                { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") },
+                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match() }
+            )
+        }
+
+    }
+
+    test("human - vcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches', checkIfExists: true)
+                        ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/gatk4/applyvqsr/tests/main.nf.test.snap

@@ -0,0 +1,95 @@
+{
+    "human - vcf": {
+        "content": [
+            "test.vcf.gz.tbi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-15T13:31:50.727658"
+    },
+    "human - vcf - allele-specific": {
+        "content": [
+            "test.vcf.gz.tbi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-15T13:29:42.331816"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,4a6890d486a62ce6f2edfd2f8961da4f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-15T13:00:49.353138"
+    },
+    "human - vcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,4a6890d486a62ce6f2edfd2f8961da4f"
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4a6890d486a62ce6f2edfd2f8961da4f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-15T13:01:24.370421"
+    },
+    "versions_allelspecific": {
+        "content": [
+            [
+                "versions.yml:md5,4a6890d486a62ce6f2edfd2f8961da4f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-15T13:01:08.104194"
+    }
+}

modules/nf-core/gatk4/applyvqsr/tests/no-allelspecificity.config

@@ -0,0 +1,5 @@
+process {
+    withName: GATK4_APPLYVQSR {
+        ext.args = '--mode SNP --truth-sensitivity-filter-level 99.0'
+    }
+}

modules/nf-core/gatk4/applyvqsr/tests/tags.yml

@@ -0,0 +1,2 @@
+gatk4/applyvqsr:
+  - "modules/nf-core/gatk4/applyvqsr/**"

tests/config/pytest_modules.yml

@@ -582,9 +582,6 @@ gatk/realignertargetcreator:
 gatk/unifiedgenotyper:
   - modules/nf-core/gatk/unifiedgenotyper/**
   - tests/modules/nf-core/gatk/unifiedgenotyper/**
-gatk4/applyvqsr:
-  - modules/nf-core/gatk4/applyvqsr/**
-  - tests/modules/nf-core/gatk4/applyvqsr/**
 gatk4/calibratedragstrmodel:
   - modules/nf-core/gatk4/calibratedragstrmodel/**
   - tests/modules/nf-core/gatk4/calibratedragstrmodel/**