Add regions bed and nf-test to glnexus (nf-core#6888)

Add regions and nf-test to glnexus

Co-authored-by: Sateesh_Peri <[email protected]>

modules/nf-core/glnexus/main.nf

@@ -1,6 +1,6 @@
 process GLNEXUS {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_high'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -9,6 +9,7 @@ process GLNEXUS {
 
     input:
     tuple val(meta), path(gvcfs)
+    tuple val(meta2), path(bed)
 
     output:
     tuple val(meta), path("*.bcf"), emit: bcf
@@ -20,6 +21,7 @@ process GLNEXUS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def regions = bed ? "--bed ${bed}" : ""
 
     // Make list of GVCFs to merge
     def input = gvcfs.collect { it.toString() }
@@ -33,6 +35,7 @@ process GLNEXUS {
     glnexus_cli \\
         --threads $task.cpus \\
         --mem-gbytes $avail_mem \\
+        $regions \\
         $args \\
         ${input.join(' ')} \\
         > ${prefix}.bcf

modules/nf-core/glnexus/meta.yml

@@ -23,6 +23,15 @@ input:
         type: list
         description: Input genomic vcf files
         pattern: "*.{gvcf,gvcf.gz,g.vcf,g.vcf.gz}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing regions information
+          e.g. [ id:'test' ]
+    - bed:
+        type: list
+        description: Input BED file
+        pattern: "*.bed"
 output:
   - bcf:
       - meta:

modules/nf-core/glnexus/tests/main.nf.test

@@ -0,0 +1,97 @@
+nextflow_process {
+
+    name "Test Process GLNEXUS"
+    script "../main.nf"
+    process "GLNEXUS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "glnexus"
+
+    test("vcfs, []") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true),
+                    ]
+                ])
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("vcfs, bed") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true),
+                    ]
+                ])
+                input[1] = [
+                    [ id:'region' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("vcfs, bed - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true),
+                    ]
+                ])
+                input[1] = [
+                    [ id:'region' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/glnexus/tests/main.nf.test.snap

@@ -0,0 +1,101 @@
+{
+    "vcfs, bed - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-29T12:17:01.253378301"
+    },
+    "vcfs, bed": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-29T12:16:53.859544065"
+    },
+    "vcfs, []": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-29T12:13:03.068397129"
+    }
+}

tests/config/pytest_modules.yml

@@ -263,9 +263,6 @@ gfastats:
 gget/gget:
   - modules/nf-core/gget/gget/**
   - tests/modules/nf-core/gget/gget/**
-glnexus:
-  - modules/nf-core/glnexus/**
-  - tests/modules/nf-core/glnexus/**
 gprofiler2/gost:
   - modules/nf-core/gprofiler2/gost/**
   - tests/modules/nf-core/gprofiler2/gost/**