add nf-test and fix stub happy/sompy (#6285)

* add nf-test and fix stub * renew snapshot * simpler match --------- Co-authored-by: Simon Pearce <[email protected]>
nf-core · Aug 26, 2024 · 5f5f9f7 · 5f5f9f7
1 parent 88ae684
commit 5f5f9f7
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diff --git a/modules/nf-core/happy/sompy/main.nf b/modules/nf-core/happy/sompy/main.nf
@@ -54,7 +54,7 @@ process HAPPY_SOMPY {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = '0.3.14' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     touch ${prefix}.features.csv

diff --git a/modules/nf-core/happy/sompy/meta.yml b/modules/nf-core/happy/sompy/meta.yml
@@ -13,15 +13,39 @@ tools:
       homepage: "https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html"
       documentation: "https://github.com/Illumina/hap.py/blob/master/doc/sompy.md"
       tool_dev_url: "https://github.com/Illumina/hap.py"
-
-      licence: "['BSD-2-clause']"
+      licence: ["BSD-2-clause"]
 
 input:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing fasta file information
+        e.g. [ id:'test2']
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing fai file information
+        e.g. [ id:'test3']
+  - meta4:
+      type: map
+      description: |
+        Groovy Map containing false_positives_bed file information
+        e.g. [ id:'test4']
+  - meta5:
+      type: map
+      description: |
+        Groovy Map containing ambiguous_beds file information
+        e.g. [ id:'test5']
+  - meta6:
+      type: map
+      description: |
+        Groovy Map containing bam file information
+        e.g. [ id:'test6']
   - query_vcf:
       type: file
       description: VCF/GVCF file to query

diff --git a/modules/nf-core/happy/sompy/tests/main.nf.test b/modules/nf-core/happy/sompy/tests/main.nf.test
@@ -0,0 +1,127 @@
+nextflow_process {
+
+    name "Test Process HAPPY_SOMPY"
+    script "../main.nf"
+    process "HAPPY_SOMPY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "happy"
+    tag "happy/sompy"
+
+    test("homo_sapiens - vcf") {
+        config './nextflow.config'
+        when {
+            process {
+                """
+                input[0] = [
+                        [ id:'test' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true),
+                        []
+                        ]
+                input[1] = [
+                        [ id:'test2' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                        ]
+                input[2] = [
+                        [ id:'test3' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                        ]
+                input[3] = [[],[]]
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.stats,
+                process.out.versions,
+                file(process.out.metrics[0][1]).name,
+                file(process.out.features[0][1]).name).match()}
+            )
+        }
+
+    }
+    test("homo_sapiens - vcf - bam") {
+        config './nextflow.config'
+        when {
+            process {
+                """
+                input[0] = [
+                        [ id:'test' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true),
+                        []
+                        ]
+                input[1] = [
+                        [ id:'test2' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                        ]
+                input[2] = [
+                        [ id:'test3' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                        ]
+                input[3] = [[],[]]
+                input[4] = [[],[]]
+                input[5] = [[ id:'test2' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true)]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.stats,
+                process.out.versions,
+                file(process.out.metrics[0][1]).name,
+                file(process.out.features[0][1]).name).match()}
+            )
+        }
+
+    }
+    test("homo_sapiens - vcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                        [ id:'test' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true),
+                        []
+                        ]
+                input[1] = [
+                        [ id:'test2' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                        ]
+                input[2] = [
+                        [ id:'test3' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                        ]
+                input[3] = [[],[]]
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/happy/sompy/tests/main.nf.test.snap b/modules/nf-core/happy/sompy/tests/main.nf.test.snap
@@ -0,0 +1,111 @@
+{
+    "homo_sapiens - vcf": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.stats.csv:md5,8b35dd00bf7b5bd697a05d73fb8c0816"
+                ]
+            ],
+            [
+                "versions.yml:md5,dda929752e25faa5e5dc8e82228980fc"
+            ],
+            "test.metrics.json",
+            "test.features.csv"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T08:56:57.589412212"
+    },
+    "homo_sapiens - vcf - bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.stats.csv:md5,5e9aae3e92641f1934c10fe88f250e59"
+                ]
+            ],
+            [
+                "versions.yml:md5,dda929752e25faa5e5dc8e82228980fc"
+            ],
+            "test.metrics.json",
+            "test.features.csv"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T08:57:13.752402851"
+    },
+    "homo_sapiens - vcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.features.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.metrics.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.stats.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,dda929752e25faa5e5dc8e82228980fc"
+                ],
+                "features": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.features.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "metrics": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.metrics.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.stats.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,dda929752e25faa5e5dc8e82228980fc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T14:39:09.160343644"
+    }
+}
diff --git a/modules/nf-core/happy/sompy/tests/nextflow.config b/modules/nf-core/happy/sompy/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: HAPPY_SOMPY {
+        ext.args = '--feature-table hcc.mutect.snv'
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -617,9 +617,6 @@ haplocheck:
 haplogrep2/classify:
   - modules/nf-core/haplogrep2/classify/**
   - tests/modules/nf-core/haplogrep2/classify/**
-happy/sompy:
-  - modules/nf-core/happy/sompy/**
-  - tests/modules/nf-core/happy/sompy/**
 hicap:
   - modules/nf-core/hicap/**
   - tests/modules/nf-core/hicap/**

diff --git a/tests/modules/nf-core/happy/sompy/main.nf b/tests/modules/nf-core/happy/sompy/main.nf
diff --git a/tests/modules/nf-core/happy/sompy/nextflow.config b/tests/modules/nf-core/happy/sompy/nextflow.config