Swap verifybamid2 to nf-test (#6824)

* Swap verifybamid2 to nf-test * Update snapshots * Remove empty md5sum --------- Co-authored-by: Adam Talbot <[email protected]>
nf-core · Nov 20, 2024 · af27a50 · af27a50
1 parent 64eef62
commit af27a50
Show file tree

Hide file tree

Showing 7 changed files with 245 additions and 127 deletions.
diff --git a/modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test b/modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test
@@ -0,0 +1,98 @@
+nextflow_process {
+
+    name "Test Process VERIFYBAMID_VERIFYBAMID2"
+    script "../main.nf"
+    process "VERIFYBAMID_VERIFYBAMID2"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "verifybamid"
+    tag "verifybamid/verifybamid2"
+
+    test("Should run with SVD input") {
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ],
+                             file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam'),
+                             file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai') ]
+                input[1] = [ file(params.modules_testdata_base_path + 'delete_me/verifybamid/test.genome.vcf.UD'),
+                             file(params.modules_testdata_base_path + 'delete_me/verifybamid/test.genome.vcf.mu'),
+                             file(params.modules_testdata_base_path + 'delete_me/verifybamid/test.genome.vcf.bed') ]
+                input[2] = []
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta')
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("Should run with RefVCF input") {
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ],
+                             file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam'),
+                             file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai') ]
+                input[1] = [ [], [], [] ]
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf')
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta')
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log[0][1]).name,
+                    process.out.bed,
+                    process.out.mu,
+                    process.out.self_sm,
+                    process.out.ancestry,
+                    process.out.versions,
+                    file(process.out.ud[0][1]).name
+                    ).match() }
+            )
+        }
+    }
+
+    test("Should run with panel input") {
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ],
+                             file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam'),
+                             file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai') ]
+                input[1] = [ file(params.modules_testdata_base_path + 'delete_me/verifybamid/test.genome.vcf.UD'),
+                             file(params.modules_testdata_base_path + 'delete_me/verifybamid/test.genome.vcf.mu'),
+                             file(params.modules_testdata_base_path + 'delete_me/verifybamid/test.genome.vcf.bed') ]
+                input[2] = []
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta')
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log[0][1]).name,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test.snap b/modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test.snap
@@ -0,0 +1,142 @@
+{
+    "Should run with panel input": {
+        "content": [
+            "test.log",
+            [
+                "versions.yml:md5,199f2e02b570926d6a249055c917c6b1"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-22T13:02:25.962766167"
+    },
+    "Should run with SVD input": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.log:md5,32a9811d143450f9f5b99c21b6ecff61"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+
+                ],
+                "3": [
+
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "result.selfSM:md5,9a10860a7e79e393c773aa801ec9f84a"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "result.Ancestry:md5,fe39ad1aced7cbb1eb21a74332389ad2"
+                    ]
+                ],
+                "6": [
+                    "versions.yml:md5,199f2e02b570926d6a249055c917c6b1"
+                ],
+                "ancestry": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "result.Ancestry:md5,fe39ad1aced7cbb1eb21a74332389ad2"
+                    ]
+                ],
+                "bed": [
+
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.log:md5,32a9811d143450f9f5b99c21b6ecff61"
+                    ]
+                ],
+                "mu": [
+
+                ],
+                "self_sm": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "result.selfSM:md5,9a10860a7e79e393c773aa801ec9f84a"
+                    ]
+                ],
+                "ud": [
+
+                ],
+                "versions": [
+                    "versions.yml:md5,199f2e02b570926d6a249055c917c6b1"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-05T20:51:39.853534509"
+    },
+    "Should run with RefVCF input": {
+        "content": [
+            "test.log",
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.genome.vcf.bed:md5,47106c764019ee359b1936410e2efa1e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.genome.vcf.mu:md5,0810db02af2a176fa5ddc0f404911b66"
+                ]
+            ],
+            [
+
+            ],
+            [
+
+            ],
+            [
+                "versions.yml:md5,199f2e02b570926d6a249055c917c6b1"
+            ],
+            "test.genome.vcf.UD"
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-20T13:43:20.984216864"
+    }
+}
diff --git a/modules/nf-core/verifybamid/verifybamid2/tests/nextflow.config b/modules/nf-core/verifybamid/verifybamid2/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'VERIFYBAMID_VERIFYBAMID2' {
+        ext.args = '--DisableSanityCheck'
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -711,9 +711,6 @@ varlociraptor/preprocess:
 vcflib/vcfbreakmulti:
   - modules/nf-core/vcflib/vcfbreakmulti/**
   - tests/modules/nf-core/vcflib/vcfbreakmulti/**
-verifybamid/verifybamid2:
-  - modules/nf-core/verifybamid/verifybamid2/**
-  - tests/modules/nf-core/verifybamid/verifybamid2/**
 vrhyme/extractunbinned:
   - modules/nf-core/vrhyme/extractunbinned/**
   - tests/modules/nf-core/vrhyme/extractunbinned/**

diff --git a/tests/modules/nf-core/verifybamid/verifybamid2/main.nf b/tests/modules/nf-core/verifybamid/verifybamid2/main.nf
diff --git a/tests/modules/nf-core/verifybamid/verifybamid2/nextflow.config b/tests/modules/nf-core/verifybamid/verifybamid2/nextflow.config
diff --git a/tests/modules/nf-core/verifybamid/verifybamid2/test.yml b/tests/modules/nf-core/verifybamid/verifybamid2/test.yml