Bump genmod and add stub tests (nf-core#6846)

Co-authored-by: Sateesh_Peri <[email protected]>
maxulysse · Oct 28, 2024 · 91a84f9 · 91a84f9
1 parent cc64e71
commit 91a84f9
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Showing 16 changed files with 335 additions and 24 deletions.
diff --git a/modules/nf-core/genmod/annotate/environment.yml b/modules/nf-core/genmod/annotate/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::genmod=3.8.3
+  - bioconda::genmod=3.9
diff --git a/modules/nf-core/genmod/annotate/main.nf b/modules/nf-core/genmod/annotate/main.nf
@@ -4,15 +4,15 @@ process GENMOD_ANNOTATE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.8.3--pyhdfd78af_0':
-        'biocontainers/genmod:3.8.3--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.9--pyhdfd78af_0':
+        'biocontainers/genmod:3.9--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)
 
     output:
     tuple val(meta), path("*_annotate.vcf"), emit: vcf
-    path "versions.yml"           , emit: versions
+    path "versions.yml"                    , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/nf-core/genmod/annotate/tests/main.nf.test b/modules/nf-core/genmod/annotate/tests/main.nf.test
@@ -24,8 +24,35 @@ nextflow_process {
 
         then {
             assertAll(
-            {assert process.success},
-            {assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.2")}
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    path(process.out.vcf.get(0).get(1)).vcf.summary,
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("genmod_annotate - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/genmod.vcf.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
 

diff --git a/modules/nf-core/genmod/annotate/tests/main.nf.test.snap b/modules/nf-core/genmod/annotate/tests/main.nf.test.snap
@@ -0,0 +1,50 @@
+{
+    "genmod_annotate": {
+        "content": [
+            [
+                "versions.yml:md5,6ce3597967a536ab027d02f75d02056c"
+            ],
+            "VcfFile [chromosomes=[1], sampleCount=3, variantCount=57, phased=false, phasedAutodetect=false]"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-25T11:44:57.176895794"
+    },
+    "genmod_annotate - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_annotate.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,6ce3597967a536ab027d02f75d02056c"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_annotate.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6ce3597967a536ab027d02f75d02056c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-25T11:49:16.409331019"
+    }
+}
diff --git a/modules/nf-core/genmod/compound/environment.yml b/modules/nf-core/genmod/compound/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::genmod=3.8.3
+  - bioconda::genmod=3.9
diff --git a/modules/nf-core/genmod/compound/main.nf b/modules/nf-core/genmod/compound/main.nf
@@ -4,15 +4,15 @@ process GENMOD_COMPOUND {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.8.3--pyhdfd78af_0':
-        'biocontainers/genmod:3.8.3--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.9--pyhdfd78af_0':
+        'biocontainers/genmod:3.9--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)
 
     output:
     tuple val(meta), path("*_compound.vcf"), emit: vcf
-    path "versions.yml"           , emit: versions
+    path "versions.yml"                    , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/nf-core/genmod/compound/tests/main.nf.test b/modules/nf-core/genmod/compound/tests/main.nf.test
@@ -23,8 +23,35 @@ nextflow_process {
 
         then {
             assertAll(
-            {assert process.success},
-            {assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.2")}
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    path(process.out.vcf.get(0).get(1)).vcf.summary,
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("genmod_compound - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/genmod_compound.vcf', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
 

diff --git a/modules/nf-core/genmod/compound/tests/main.nf.test.snap b/modules/nf-core/genmod/compound/tests/main.nf.test.snap
@@ -0,0 +1,50 @@
+{
+    "genmod_compound": {
+        "content": [
+            [
+                "versions.yml:md5,822fb501a48a6f8c28ba8f678d27ba2e"
+            ],
+            "VcfFile [chromosomes=[MT], sampleCount=3, variantCount=22, phased=false, phasedAutodetect=false]"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-25T11:49:41.417545149"
+    },
+    "genmod_compound - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_compound.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,822fb501a48a6f8c28ba8f678d27ba2e"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_compound.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,822fb501a48a6f8c28ba8f678d27ba2e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-25T11:49:48.678803012"
+    }
+}
diff --git a/modules/nf-core/genmod/models/environment.yml b/modules/nf-core/genmod/models/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::genmod=3.8.3
+  - bioconda::genmod=3.9
diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf
@@ -4,8 +4,8 @@ process GENMOD_MODELS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.8.3--pyhdfd78af_0':
-        'biocontainers/genmod:3.8.3--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.9--pyhdfd78af_0':
+        'biocontainers/genmod:3.9--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)
@@ -14,7 +14,7 @@ process GENMOD_MODELS {
 
     output:
     tuple val(meta), path("*_models.vcf"), emit: vcf
-    path "versions.yml"           , emit: versions
+    path "versions.yml"                  , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/nf-core/genmod/models/tests/main.nf.test b/modules/nf-core/genmod/models/tests/main.nf.test
@@ -25,11 +25,39 @@ nextflow_process {
 
         then {
             assertAll(
-            {assert process.success},
-            {assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.2")}
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    path(process.out.vcf.get(0).get(1)).vcf.summary,
+                    ).match() }
             )
         }
 
     }
 
+    test("genmod_models - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test_annotate.vcf.gz', checkIfExists: true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true)
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
 }
diff --git a/modules/nf-core/genmod/models/tests/main.nf.test.snap b/modules/nf-core/genmod/models/tests/main.nf.test.snap
@@ -0,0 +1,50 @@
+{
+    "genmod_models - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_models.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,10442b1602069000967f51837d7b5b63"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_models.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,10442b1602069000967f51837d7b5b63"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-25T11:51:04.841425679"
+    },
+    "genmod_models": {
+        "content": [
+            [
+                "versions.yml:md5,10442b1602069000967f51837d7b5b63"
+            ],
+            "VcfFile [chromosomes=[1], sampleCount=3, variantCount=57, phased=false, phasedAutodetect=false]"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-25T11:49:56.642318737"
+    }
+}
diff --git a/modules/nf-core/genmod/score/environment.yml b/modules/nf-core/genmod/score/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::genmod=3.8.3
+  - bioconda::genmod=3.9
diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf
@@ -4,8 +4,8 @@ process GENMOD_SCORE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.8.3--pyhdfd78af_0':
-        'biocontainers/genmod:3.8.3--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.9--pyhdfd78af_0':
+        'biocontainers/genmod:3.9--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)
@@ -14,7 +14,7 @@ process GENMOD_SCORE {
 
     output:
     tuple val(meta), path("*_score.vcf"), emit: vcf
-    path "versions.yml"           , emit: versions
+    path "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when