port gridss/gridss to nf-test

modules/nf-core/gridss/gridss/main.nf

@@ -8,14 +8,13 @@ process GRIDSS_GRIDSS {
         'biocontainers/gridss:2.13.2--h270b39a_0' }"
 
     input:
-    tuple val(meta), path(inputs), path(assembly)
+    tuple val(meta) , path(inputs)
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(fasta_fai)
     tuple val(meta4), path(bwa_index)
 
     output:
-    tuple val(meta), path("*.vcf.gz")       , emit: vcf, optional:true
-    tuple val(meta), path("*.assembly.bam") , emit: assembly, optional:true
+    tuple val(meta), path("*.vcf.gz")       , emit: vcf
     path "versions.yml"                     , emit: versions
 
     when:
@@ -26,7 +25,6 @@ process GRIDSS_GRIDSS {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = '2.13.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
-    def assembly_bam = assembly ? "--assembly ${assembly}" : ""
     def bwa = bwa_index ? "cp -s ${bwa_index}/* ." : ""
 
     """
@@ -36,7 +34,6 @@ process GRIDSS_GRIDSS {
         --output ${prefix}.vcf.gz \\
         --reference ${fasta} \\
         --threads ${task.cpus} \\
-        ${assembly} \\
         --jvmheap ${task.memory.toGiga() - 1}g \\
         --otherjvmheap ${task.memory.toGiga() - 1}g \\
         ${inputs}
@@ -55,11 +52,9 @@ process GRIDSS_GRIDSS {
     def steps = args.contains("-s ") ? args.split('-s ')[-1].split(" ")[0] :
                 args.contains("--steps ") ? args.split('--steps ')[-1].split(" ")[0] :
                 "all"
-    def vcf = steps.contains("call") || steps.contains("all") ? "touch ${prefix}.vcf.gz" : ""
-    def assembly_bam = steps.contains("assembly") || steps.contains("all") ? "touch ${prefix}.assembly.bam" : ""
+    def vcf = steps.contains("call") || steps.contains("all") ? "echo '' | gzip > ${prefix}.vcf.gz" : ""
     """
     ${vcf}
-    ${assembly_bam}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/gridss/gridss/meta.yml

@@ -7,26 +7,22 @@ keywords:
   - cram
   - vcf
 tools:
-  - "gridss":
+  - gridss:
       description: "GRIDSS: the Genomic Rearrangement IDentification Software Suite"
       documentation: "https://github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation"
       tool_dev_url: "https://github.com/PapenfussLab/gridss"
       doi: "10.1186/s13059-021-02423-x"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
+        e.g. [ id:'test']
   - inputs:
-      type: file(s)
+      type: file
       description: One or more input BAM/CRAM file(s)
       pattern: "*.{bam,cram}"
-  - assembly:
-      type: file
-      description: OPTIONAL - An assembly BAM file created by the assembly step of Gridss
-      pattern: "*.bam"
   - fasta:
       type: file
       description: The reference fasta
@@ -43,7 +39,7 @@ output:
       type: map
       description: |
         Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
+        e.g. [ id:'test' ]
   - versions:
       type: file
       description: File containing software versions
@@ -52,10 +48,6 @@ output:
       type: file
       description: The called VCF file created by Gridss' call step
       pattern: "*.vcf.gz"
-  - assembly:
-      type: file
-      description: The assembly BAM file created by Gridss' assembly step
-      pattern: "*.assembly.bam"
 authors:
   - "@nvnieuwk"
 maintainers:

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

@@ -0,0 +1,145 @@
+nextflow_process {
+
+    name "Test Process GRIDSS_GRIDSS"
+    script "../main.nf"
+    process "GRIDSS_GRIDSS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gridss"
+    tag "gridss/gridss"
+    tag "bwa/index"
+
+    setup {
+
+        run("BWA_INDEX") {
+            script "../../../bwa/index/main.nf"
+            process {
+                """
+                input[0] = [ [id:'fasta'],
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                        ]
+                """
+            }
+        }
+
+    }
+
+    test("human - bam - bwa") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                        file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), //inputs
+                        ]
+                input[1] = [ [id:'fasta'],
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                        ]
+                input[2] = [ [id:'fasta_fai'],
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                        ]
+                input[3] = BWA_INDEX.out.index
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() },
+                { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") }
+            )
+        }
+
+    }
+
+    test("human - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                        file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), //inputs
+                        ]
+                input[1] = [ [id:'fasta'],
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                        ]
+                input[2] = [ [id:'fasta_fai'],
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                        ]
+                input[3] = [ [], [] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() },
+                { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") }
+            )
+        }
+
+    }
+
+    test("human - cram") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), //inputs
+                        ]
+                input[1] = [ [id:'fasta'],
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                        ]
+                input[2] = [ [id:'fasta_fai'],
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                        ]
+                input[3] = [ [], [] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() },
+                { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") }
+            )
+        }
+
+    }
+
+    test("human - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                        file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), //inputs
+                        ]
+                input[1] = [ [id:'fasta'],
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                        ]
+                input[2] = [ [id:'fasta_fai'],
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                        ]
+                input[3] = [ [], [] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

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

@@ -0,0 +1,83 @@
+{
+    "human - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,139867df5d7eaf22a89ae574f08e8d80"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,139867df5d7eaf22a89ae574f08e8d80"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-10T11:48:56.7778"
+    },
+    "human - bam - bwa": {
+        "content": [
+            [
+                "versions.yml:md5,139867df5d7eaf22a89ae574f08e8d80"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-10T11:47:23.943354"
+    },
+    "human - bam": {
+        "content": [
+            [
+                "versions.yml:md5,139867df5d7eaf22a89ae574f08e8d80"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-10T11:48:06.074469"
+    },
+    "human - cram": {
+        "content": [
+            [
+                "versions.yml:md5,139867df5d7eaf22a89ae574f08e8d80"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-10T11:48:45.270441"
+    },
+    "human - bam - assembly": {
+        "content": [
+            [
+                "versions.yml:md5,139867df5d7eaf22a89ae574f08e8d80"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-09T14:13:21.550069"
+    }
+}

modules/nf-core/gridss/gridss/tests/tags.yml

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

tests/config/pytest_modules.yml

@@ -659,9 +659,6 @@ graphtyper/vcfconcatenate:
 grids/gridsssomaticfilter:
   - modules/nf-core/grids/gridsssomaticfilter/**
   - tests/modules/nf-core/grids/gridsssomaticfilter/**
-gridss/gridss:
-  - modules/nf-core/gridss/gridss/**
-  - tests/modules/nf-core/gridss/gridss/**
 gridss/gridssgenerateponbedpe:
   - modules/nf-core/gridss/gridssgenerateponbedpe/**
   - tests/modules/nf-core/gridss/gridssgenerateponbedpe/**