Gridss environment files / port to nf-test (#5932)

* add env files * modify meta * update names and port to nf-test * remove pytest * update tests and meta, remove obsolete folders * prettier * just test filenames * update tests * Update nftest * Working gridss/somaticfilter * Update snapshot * Simplify nf-test code --------- Co-authored-by: Maxime U Garcia <[email protected]> Co-authored-by: Simon Pearce <[email protected]>
nf-core · Jan 17, 2025 · 1f2b32d · 1f2b32d
1 parent e9b59c8
commit 1f2b32d
Show file tree

Hide file tree

Showing 24 changed files with 493 additions and 210 deletions.
diff --git a/modules/nf-core/gridss/generateponbedpe/environment.yml b/modules/nf-core/gridss/generateponbedpe/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::gridss=2.13.2
diff --git a/...ore/gridss/gridssgenerateponbedpe/main.nf → ...s/nf-core/gridss/generateponbedpe/main.nf b/...ore/gridss/gridssgenerateponbedpe/main.nf → ...s/nf-core/gridss/generateponbedpe/main.nf
@@ -1,14 +1,14 @@
-process GRIDSS_GRIDSSGENERATEPONBEDPE {
+process GRIDSS_GENERATEPONBEDPE {
     tag "$meta.id"
     label 'process_high'
 
-    conda "bioconda::gridss=2.13.2"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gridss:2.13.2--h270b39a_0':
         'biocontainers/gridss:2.13.2--h270b39a_0' }"
 
     input:
-    tuple val(meta),  path(vcf), path(bedpe), path(bed)
+    tuple val(meta) , path(vcf), path(bedpe), path(bed)
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(fai)
     tuple val(meta4), path(bwa_index)
@@ -24,18 +24,17 @@ process GRIDSS_GRIDSSGENERATEPONBEDPE {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def vcf = vcf ? "INPUT=${vcf}" : ""
-    def bedpe = bedpe ? "INPUT_BEDPE=${bedpe}" : ""
-    def bed   = bed ? "INPUT_BED=${bed}" : ""
+    def vcf_command = vcf ? "INPUT=${vcf}" : ""
+    def bedpe_command = bedpe ? "INPUT_BEDPE=${bedpe}" : ""
+    def bed_command   = bed ? "INPUT_BED=${bed}" : ""
     def bwa = bwa_index ? "cp -s ${bwa_index}/* ." : ""
     def ref = bwa_index ? "REFERENCE_SEQUENCE=${fasta}" : ""
-
     """
     ${bwa}
     GeneratePonBedpe \\
-        ${vcf} \\
-        ${bedpe} \\
-        ${bed} \\
+        ${vcf_command} \\
+        ${bedpe_command} \\
+        ${bed_command} \\
         ${ref} \\
         OUTPUT_BEDPE=${prefix}.bedpe \\
         OUTPUT_BED=${prefix}.bed \\
@@ -47,6 +46,7 @@ process GRIDSS_GRIDSSGENERATEPONBEDPE {
         GeneratePonBedpe: \$(echo \$(GeneratePonBedpe --version 2>&1))
     END_VERSIONS
     """
+
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """

diff --git a/...re/gridss/gridssgenerateponbedpe/meta.yml → .../nf-core/gridss/generateponbedpe/meta.yml b/...re/gridss/gridssgenerateponbedpe/meta.yml → .../nf-core/gridss/generateponbedpe/meta.yml
@@ -1,4 +1,4 @@
-name: "gridss_gridssgenerateponbedpe"
+name: "gridss_generateponbedpe"
 description: GRIDSS is a module software suite containing tools useful for the detection
   of genomic rearrangements.
 keywords:
@@ -8,14 +8,12 @@ keywords:
   - bed
   - 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"]
-
       identifier: biotools:gridss
 input:
   - - meta:
@@ -60,8 +58,8 @@ input:
           e.g. [ id:'test']
     - bwa_index:
         type: directory
-        description: OPTIONAL - The BWA index created from the reference fasta, will
-          be generated by Gridss in the setupreference step
+        description: OPTIONAL - The BWA index created from the reference fasta, will be generated by Gridss in the setupreference step
+
 output:
   - bedpe:
       - meta:
@@ -90,3 +88,5 @@ output:
           pattern: "versions.yml"
 authors:
   - "@kubranarci"
+maintainers:
+  - "@famosab"
diff --git a/modules/nf-core/gridss/generateponbedpe/tests/main.nf.test b/modules/nf-core/gridss/generateponbedpe/tests/main.nf.test
@@ -0,0 +1,107 @@
+nextflow_process {
+
+    name "Test Process GRIDSS_GENERATEPONBEDPE"
+    script "../main.nf"
+    process "GRIDSS_GENERATEPONBEDPE"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gridss"
+    tag "gridss/generateponbedpe"
+    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)
+                        ]
+                """
+            }
+        }
+
+        run("GRIDSS_GRIDSS") {
+            script "../../../gridss/gridss/main.nf"
+            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
+                        [] //assembly
+                        ]
+                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
+                """
+            }
+        }
+
+    }
+
+    test("human - vcf") {
+
+        when {
+            process {
+                """
+                input[0] = GRIDSS_GRIDSS.out.vcf.map{ it -> tuple( it[0], it[1], [], [] ) }
+                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,
+                    file(process.out.bed.get(0).get(1)).name,
+                    file(process.out.bedpe.get(0).get(1)).name
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("human - vcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = GRIDSS_GRIDSS.out.vcf.map{ it -> tuple( it[0], it[1], [], [] ) }
+                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).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/gridss/generateponbedpe/tests/main.nf.test.snap b/modules/nf-core/gridss/generateponbedpe/tests/main.nf.test.snap
@@ -0,0 +1,65 @@
+{
+    "human - vcf": {
+        "content": [
+            [
+                "versions.yml:md5,645a222948827e5376957f8b60fc2a05"
+            ],
+            "test.bed",
+            "test.bedpe"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-02T10:51:47.865144"
+    },
+    "human - vcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bedpe:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,645a222948827e5376957f8b60fc2a05"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bedpe": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bedpe:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,645a222948827e5376957f8b60fc2a05"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-09T16:56:29.984471332"
+    }
+}
diff --git a/modules/nf-core/gridss/generateponbedpe/tests/nextflow.config b/modules/nf-core/gridss/generateponbedpe/tests/nextflow.config
@@ -0,0 +1,8 @@
+process {
+    withName: BWA_INDEX {
+            ext.prefix = 'genome.fasta'
+    }
+    withName: GRIDSS_GENERATEPONBEDPE {
+            ext.args = 'NORMAL_ORDINAL=1 MIN_BREAKPOINT_QUAL=10'
+    }
+}
diff --git a/modules/nf-core/gridss/generateponbedpe/tests/tags.yml b/modules/nf-core/gridss/generateponbedpe/tests/tags.yml
@@ -0,0 +1,2 @@
+gridss/generateponbedpe:
+  - "modules/nf-core/gridss/generateponbedpe/**"
diff --git a/modules/nf-core/gridss/gridss/main.nf b/modules/nf-core/gridss/gridss/main.nf
@@ -36,6 +36,7 @@ process GRIDSS_GRIDSS {
         --threads ${task.cpus} \\
         --jvmheap ${task.memory.toGiga() - 1}g \\
         --otherjvmheap ${task.memory.toGiga() - 1}g \\
+        $args \\
         ${inputs}
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/gridss/gridss/tests/main.nf.test b/modules/nf-core/gridss/gridss/tests/main.nf.test
@@ -45,10 +45,12 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out.versions).match() },
-                { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") }
+                { assert snapshot(
+                    path(process.out.vcf.get(0).get(1)).vcf.summary, // no SVs exist in the test data
+                    process.out.versions
+                    ).match() }
             )
         }
 
@@ -74,10 +76,12 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out.versions).match() },
-                { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") }
+                { assert snapshot(
+                    path(process.out.vcf.get(0).get(1)).vcf.summary, // no SVs exist in the test data
+                    process.out.versions
+                    ).match() }
             )
         }
 
@@ -103,10 +107,12 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out.versions).match() },
-                { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") }
+                { assert snapshot(
+                    path(process.out.vcf.get(0).get(1)).vcf.summary, // no SVs exist in the test data
+                    process.out.versions
+                    ).match() }
             )
         }
 
@@ -134,8 +140,8 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
                 { assert snapshot(process.out).match() }
             )
         }
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		gridss/generateponbedpe:
		- "modules/nf-core/gridss/generateponbedpe/**"