update bismark v0.24.2, rm input stageAs, add stub, update tests+snap

nf-core · Oct 12, 2024 · 5f26cab · 5f26cab
1 parent 7fd374e
commit 5f26cab
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Showing 6 changed files with 156 additions and 58 deletions.
diff --git a/modules/nf-core/bismark/genomepreparation/environment.yml b/modules/nf-core/bismark/genomepreparation/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bismark=0.24.0
+  - bioconda::bismark=0.24.2
diff --git a/modules/nf-core/bismark/genomepreparation/main.nf b/modules/nf-core/bismark/genomepreparation/main.nf
@@ -4,22 +4,25 @@ process BISMARK_GENOMEPREPARATION {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bismark:0.24.0--hdfd78af_0' :
-        'biocontainers/bismark:0.24.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/bismark:0.24.2--hdfd78af_0' :
+        'biocontainers/bismark:0.24.2--hdfd78af_0' }"
 
     input:
-    path fasta, stageAs: "BismarkIndex/*"
+    tuple val(meta), path(fasta)
 
     output:
-    path "BismarkIndex" , emit: index
-    path "versions.yml" , emit: versions
+    tuple val(meta), path("BismarkIndex"), emit: index
+    path "versions.yml"                  , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
     """
+    mkdir BismarkIndex
+    mv $fasta BismarkIndex/
+
     bismark_genome_preparation \\
         $args \\
         BismarkIndex
@@ -29,4 +32,16 @@ process BISMARK_GENOMEPREPARATION {
         bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    """
+    mkdir BismarkIndex
+    touch BismarkIndex/$fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/bismark/genomepreparation/meta.yml b/modules/nf-core/bismark/genomepreparation/meta.yml
@@ -23,11 +23,21 @@ tools:
       licence: ["GPL-3.0-or-later"]
       identifier: biotools:bismark
 input:
-  - - fasta:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
         type: file
         description: Input genome fasta file
 output:
   - index:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
       - BismarkIndex:
           type: directory
           description: Bismark genome index directory
@@ -41,3 +51,4 @@ authors:
   - "@phue"
 maintainers:
   - "@phue"
+  - "@sateeshperi"
diff --git a/modules/nf-core/bismark/genomepreparation/tests/main.nf.test b/modules/nf-core/bismark/genomepreparation/tests/main.nf.test
@@ -3,31 +3,54 @@ nextflow_process {
     name "Test Process BISMARK_GENOMEPREPARATION"
     script "../main.nf"
     process "BISMARK_GENOMEPREPARATION"
-    tag "bismark"
-    tag "bismark/genomepreparation"
+
     tag "modules"
+    tag "bismark/genomepreparation"
+    tag "bismark"
     tag "modules_nfcore"
 
-    test("Should run bismark/genomepreparation without failures") {
+    test("sarscov2 genome [fasta]") {
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
             process {
                 """
-                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
                 """
             }
         }
 
         then {
             assertAll(
-            { assert process.success },
-            { assert snapshot(process.out).match() }
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
+    }
+
+    test("sarscov2 genome [fasta] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
 
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
     }
 
 }
diff --git a/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap b/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap
@@ -1,65 +1,116 @@
 {
-    "Should run bismark/genomepreparation without failures": {
+    "sarscov2 genome [fasta] - stub": {
         "content": [
             {
                 "0": [
                     [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "genome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,4d9a42530334575b18a6bde4ae72f7d6"
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "genome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4d9a42530334575b18a6bde4ae72f7d6"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-12T18:25:54.462607784"
+    },
+    "sarscov2 genome [fasta]": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
                         [
                             [
-                                "BS_CT.1.bt2:md5,10a8854e5eeb95629f46d24b0d8da70c",
-                                "BS_CT.2.bt2:md5,bc5d407e6fce3e1cdb4b23ab2a20f707",
-                                "BS_CT.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
-                                "BS_CT.4.bt2:md5,6c4f549575e5882ff3a97ae10ae2e7be",
-                                "BS_CT.rev.1.bt2:md5,d37d586b41b6a36efb25839961d242cb",
-                                "BS_CT.rev.2.bt2:md5,48bf400de85cd7324fbf6bf38fe2dc95",
-                                "genome_mfa.CT_conversion.fa:md5,903b9f357eea4a5f36e21e78e0fe1dfa"
+                                [
+                                    "BS_CT.1.bt2:md5,10a8854e5eeb95629f46d24b0d8da70c",
+                                    "BS_CT.2.bt2:md5,bc5d407e6fce3e1cdb4b23ab2a20f707",
+                                    "BS_CT.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
+                                    "BS_CT.4.bt2:md5,6c4f549575e5882ff3a97ae10ae2e7be",
+                                    "BS_CT.rev.1.bt2:md5,d37d586b41b6a36efb25839961d242cb",
+                                    "BS_CT.rev.2.bt2:md5,48bf400de85cd7324fbf6bf38fe2dc95",
+                                    "genome_mfa.CT_conversion.fa:md5,903b9f357eea4a5f36e21e78e0fe1dfa"
+                                ],
+                                [
+                                    "BS_GA.1.bt2:md5,a6fa4068ed10872568f32568c66cb600",
+                                    "BS_GA.2.bt2:md5,fc5b634e2f5137801e3801d62ad05f74",
+                                    "BS_GA.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
+                                    "BS_GA.4.bt2:md5,b1e855685ed634daa7df8e180c9b2fc4",
+                                    "BS_GA.rev.1.bt2:md5,17f51e65f44477962226a83b369b2bc4",
+                                    "BS_GA.rev.2.bt2:md5,d36044c5dfe37af0411f60d446585bc6",
+                                    "genome_mfa.GA_conversion.fa:md5,e529375ec2039112161465b5169fcd59"
+                                ]
                             ],
-                            [
-                                "BS_GA.1.bt2:md5,a6fa4068ed10872568f32568c66cb600",
-                                "BS_GA.2.bt2:md5,fc5b634e2f5137801e3801d62ad05f74",
-                                "BS_GA.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
-                                "BS_GA.4.bt2:md5,b1e855685ed634daa7df8e180c9b2fc4",
-                                "BS_GA.rev.1.bt2:md5,17f51e65f44477962226a83b369b2bc4",
-                                "BS_GA.rev.2.bt2:md5,d36044c5dfe37af0411f60d446585bc6",
-                                "genome_mfa.GA_conversion.fa:md5,e529375ec2039112161465b5169fcd59"
-                            ]
-                        ],
-                        "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6"
+                            "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6"
+                        ]
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,92d3bda85e8d9517fce396c615141003"
+                    "versions.yml:md5,4d9a42530334575b18a6bde4ae72f7d6"
                 ],
                 "index": [
                     [
+                        {
+                            "id": "test"
+                        },
                         [
                             [
-                                "BS_CT.1.bt2:md5,10a8854e5eeb95629f46d24b0d8da70c",
-                                "BS_CT.2.bt2:md5,bc5d407e6fce3e1cdb4b23ab2a20f707",
-                                "BS_CT.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
-                                "BS_CT.4.bt2:md5,6c4f549575e5882ff3a97ae10ae2e7be",
-                                "BS_CT.rev.1.bt2:md5,d37d586b41b6a36efb25839961d242cb",
-                                "BS_CT.rev.2.bt2:md5,48bf400de85cd7324fbf6bf38fe2dc95",
-                                "genome_mfa.CT_conversion.fa:md5,903b9f357eea4a5f36e21e78e0fe1dfa"
+                                [
+                                    "BS_CT.1.bt2:md5,10a8854e5eeb95629f46d24b0d8da70c",
+                                    "BS_CT.2.bt2:md5,bc5d407e6fce3e1cdb4b23ab2a20f707",
+                                    "BS_CT.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
+                                    "BS_CT.4.bt2:md5,6c4f549575e5882ff3a97ae10ae2e7be",
+                                    "BS_CT.rev.1.bt2:md5,d37d586b41b6a36efb25839961d242cb",
+                                    "BS_CT.rev.2.bt2:md5,48bf400de85cd7324fbf6bf38fe2dc95",
+                                    "genome_mfa.CT_conversion.fa:md5,903b9f357eea4a5f36e21e78e0fe1dfa"
+                                ],
+                                [
+                                    "BS_GA.1.bt2:md5,a6fa4068ed10872568f32568c66cb600",
+                                    "BS_GA.2.bt2:md5,fc5b634e2f5137801e3801d62ad05f74",
+                                    "BS_GA.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
+                                    "BS_GA.4.bt2:md5,b1e855685ed634daa7df8e180c9b2fc4",
+                                    "BS_GA.rev.1.bt2:md5,17f51e65f44477962226a83b369b2bc4",
+                                    "BS_GA.rev.2.bt2:md5,d36044c5dfe37af0411f60d446585bc6",
+                                    "genome_mfa.GA_conversion.fa:md5,e529375ec2039112161465b5169fcd59"
+                                ]
                             ],
-                            [
-                                "BS_GA.1.bt2:md5,a6fa4068ed10872568f32568c66cb600",
-                                "BS_GA.2.bt2:md5,fc5b634e2f5137801e3801d62ad05f74",
-                                "BS_GA.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
-                                "BS_GA.4.bt2:md5,b1e855685ed634daa7df8e180c9b2fc4",
-                                "BS_GA.rev.1.bt2:md5,17f51e65f44477962226a83b369b2bc4",
-                                "BS_GA.rev.2.bt2:md5,d36044c5dfe37af0411f60d446585bc6",
-                                "genome_mfa.GA_conversion.fa:md5,e529375ec2039112161465b5169fcd59"
-                            ]
-                        ],
-                        "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6"
+                            "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6"
+                        ]
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,92d3bda85e8d9517fce396c615141003"
+                    "versions.yml:md5,4d9a42530334575b18a6bde4ae72f7d6"
                 ]
             }
         ],
-        "timestamp": "2023-10-17T16:14:41.509500586"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-12T18:25:45.474877931"
     }
 }
diff --git a/modules/nf-core/bismark/genomepreparation/tests/tags.yml b/modules/nf-core/bismark/genomepreparation/tests/tags.yml