Added nf-test for methyldackel/extract (nf-core#6549)

* Added nf-test for methyldackel/extract * Version bump
FriederikeHanssen · Sep 4, 2024 · 1c2bf5b · 1c2bf5b
1 parent d612c28
commit 1c2bf5b
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Showing 12 changed files with 245 additions and 64 deletions.
diff --git a/modules/nf-core/methyldackel/extract/environment.yml b/modules/nf-core/methyldackel/extract/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::methyldackel=0.6.0
+  - bioconda::methyldackel=0.6.1
diff --git a/modules/nf-core/methyldackel/extract/main.nf b/modules/nf-core/methyldackel/extract/main.nf
@@ -4,8 +4,8 @@ process METHYLDACKEL_EXTRACT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0' :
-        'biocontainers/methyldackel:0.6.0--h22771d5_0' }"
+        'https://depot.galaxyproject.org/singularity/methyldackel:0.6.1--he4a0461_7' :
+        'biocontainers/methyldackel:0.6.1--he4a0461_7' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
@@ -33,4 +33,16 @@ process METHYLDACKEL_EXTRACT {
         methyldackel: \$(MethylDackel --version 2>&1 | cut -f1 -d" ")
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def out_extension = args.contains('--methylKit') ? 'methylKit' : 'bedGraph'
+    """
+    touch ${bam.baseName}_CpG.${out_extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        methyldackel: \$(MethylDackel --version 2>&1 | cut -f1 -d" ")
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/methyldackel/extract/tests/main.nf.test b/modules/nf-core/methyldackel/extract/tests/main.nf.test
@@ -0,0 +1,90 @@
+
+nextflow_process {
+
+    name "Test Process METHYLDACKEL_EXTRACT"
+    script "../main.nf"
+    process "METHYLDACKEL_EXTRACT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "methyldackel"
+    tag "methyldackel/extract"
+
+    test("test-methyldackel-extract") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true)
+                ]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-methyldackel-extract-methyl-kit") {
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true)
+                ]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-methyldackel-extract-methyl-kit-stub") {
+        config "./nextflow.config"
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true)
+                ]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/methyldackel/extract/tests/main.nf.test.snap b/modules/nf-core/methyldackel/extract/tests/main.nf.test.snap
@@ -0,0 +1,125 @@
+{
+    "test-methyldackel-extract-methyl-kit": {
+        "content": [
+            {
+                "0": [
+
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.methylated.sorted_CpG.methylKit:md5,b1dc217909cd5f8174058c7af785f51c"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,9e23b0c31bf0f98e9348321fe9226498"
+                ],
+                "bedgraph": [
+
+                ],
+                "methylkit": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.methylated.sorted_CpG.methylKit:md5,b1dc217909cd5f8174058c7af785f51c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9e23b0c31bf0f98e9348321fe9226498"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-04T20:34:17.513866"
+    },
+    "test-methyldackel-extract-methyl-kit-stub": {
+        "content": [
+            {
+                "0": [
+
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.methylated.sorted_CpG.methylKit:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,9e23b0c31bf0f98e9348321fe9226498"
+                ],
+                "bedgraph": [
+
+                ],
+                "methylkit": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.methylated.sorted_CpG.methylKit:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9e23b0c31bf0f98e9348321fe9226498"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-04T20:34:22.343382"
+    },
+    "test-methyldackel-extract": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.methylated.sorted_CpG.bedGraph:md5,abcc9d1db6e48d5aced567c337b563d4"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    "versions.yml:md5,9e23b0c31bf0f98e9348321fe9226498"
+                ],
+                "bedgraph": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.methylated.sorted_CpG.bedGraph:md5,abcc9d1db6e48d5aced567c337b563d4"
+                    ]
+                ],
+                "methylkit": [
+
+                ],
+                "versions": [
+                    "versions.yml:md5,9e23b0c31bf0f98e9348321fe9226498"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-04T20:34:12.605013"
+    }
+}
diff --git a/modules/nf-core/methyldackel/extract/tests/nextflow.config b/modules/nf-core/methyldackel/extract/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: METHYLDACKEL_EXTRACT {
+        ext.args = "--methylKit"
+    }
+}
diff --git a/modules/nf-core/methyldackel/mbias/environment.yml b/modules/nf-core/methyldackel/mbias/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::methyldackel=0.6.0
+  - bioconda::methyldackel=0.6.1
diff --git a/modules/nf-core/methyldackel/mbias/main.nf b/modules/nf-core/methyldackel/mbias/main.nf
@@ -4,8 +4,8 @@ process METHYLDACKEL_MBIAS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0' :
-        'biocontainers/methyldackel:0.6.0--h22771d5_0' }"
+        'https://depot.galaxyproject.org/singularity/methyldackel:0.6.1--he4a0461_7' :
+        'biocontainers/methyldackel:0.6.1--he4a0461_7' }"
 
     input:
     tuple val(meta), path(bam), path(bai)

diff --git a/modules/nf-core/methyldackel/mbias/tests/main.nf.test.snap b/modules/nf-core/methyldackel/mbias/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,08cbfd1c80fd6a7c1f0c46831f70bb1c"
+                    "versions.yml:md5,0d6cea2918112948708bd1c2f5309398"
                 ],
                 "txt": [
                     [
@@ -24,15 +24,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,08cbfd1c80fd6a7c1f0c46831f70bb1c"
+                    "versions.yml:md5,0d6cea2918112948708bd1c2f5309398"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-30T13:53:24.630766"
+        "timestamp": "2024-09-04T20:35:24.956573"
     },
     "test-methyldackel-mbias": {
         "content": [
@@ -44,13 +44,13 @@
                 "OT\t1\t4\t52\t3"
             ],
             [
-                "versions.yml:md5,08cbfd1c80fd6a7c1f0c46831f70bb1c"
+                "versions.yml:md5,0d6cea2918112948708bd1c2f5309398"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-30T13:53:19.7992"
+        "timestamp": "2024-09-04T20:35:20.084046"
     }
 }
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -503,9 +503,6 @@ metaphlan3/mergemetaphlantables:
 metaphlan3/metaphlan3:
   - modules/nf-core/metaphlan3/metaphlan3/**
   - tests/modules/nf-core/metaphlan3/metaphlan3/**
-methyldackel/extract:
-  - modules/nf-core/methyldackel/extract/**
-  - tests/modules/nf-core/methyldackel/extract/**
 midas/run:
   - modules/nf-core/midas/run/**
   - tests/modules/nf-core/midas/run/**

diff --git a/tests/modules/nf-core/methyldackel/extract/main.nf b/tests/modules/nf-core/methyldackel/extract/main.nf
diff --git a/tests/modules/nf-core/methyldackel/extract/nextflow.config b/tests/modules/nf-core/methyldackel/extract/nextflow.config
diff --git a/tests/modules/nf-core/methyldackel/extract/test.yml b/tests/modules/nf-core/methyldackel/extract/test.yml