Add metamap to viennarna/rnafold module (#5675)

* Add meta map to viennarna/rnafold module * Update snap
nf-core · May 25, 2024 · 8ead864 · 8ead864
1 parent 08b3605
commit 8ead864
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Showing 3 changed files with 40 additions and 13 deletions.
diff --git a/modules/nf-core/viennarna/rnafold/main.nf b/modules/nf-core/viennarna/rnafold/main.nf
@@ -8,18 +8,19 @@ process VIENNARNA_RNAFOLD {
         'biocontainers/viennarna:2.6.4--py310pl5321h6cc9453_1' }"
 
     input:
-    path fasta
+    tuple val(meta), path(fasta)
 
     output:
-    path "*.fold"         , emit: rnafold_txt
-    path "*.ps"           , emit: rnafold_ps
-    path "versions.yml"   , emit: versions
+    tuple val(meta), path("*.fold")      , emit: rnafold_txt
+    tuple val(meta), path("*.ps")        , emit: rnafold_ps
+    tuple val(meta), path("versions.yml"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = meta.id ?: "${fasta.getName()}"
     """
     RNAfold \\
         ${args} \\

diff --git a/modules/nf-core/viennarna/rnafold/tests/main.nf.test b/modules/nf-core/viennarna/rnafold/tests/main.nf.test
@@ -14,7 +14,10 @@ nextflow_process {
         when {
             process {
                 """                
-                input[0] = file(params.test_data['homo_sapiens']['genome']['transcriptome_fasta'], checkIfExists: true)
+                input[0] = [
+                    [:],
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/transcriptome.fasta", checkIfExists: true)
+                ]
                 """
             }
         }
@@ -33,8 +36,11 @@ nextflow_process {
 
         when {
             process {
-                """
-                input[0] = file(params.test_data['homo_sapiens']['genome']['transcriptome_fasta'], checkIfExists: true)
+                """                
+                input[0] = [
+                    [:],
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/transcriptome.fasta", checkIfExists: true)
+                ]
                 """
             }
         }

diff --git a/modules/nf-core/viennarna/rnafold/tests/main.nf.test.snap b/modules/nf-core/viennarna/rnafold/tests/main.nf.test.snap
@@ -2,31 +2,51 @@
     "stub": {
         "content": [
             [
-                "transcriptome.fasta.fold:md5,d41d8cd98f00b204e9800998ecf8427e"
+                [
+                    {
+
+                    },
+                    "transcriptome.fasta.fold:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
             ],
             [
-                "versions.yml:md5,76ca9d956465e05df59c27f000276284"
+                [
+                    {
+
+                    },
+                    "versions.yml:md5,76ca9d956465e05df59c27f000276284"
+                ]
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-05-22T09:28:37.785786414"
+        "timestamp": "2024-05-22T16:52:27.132604"
     },
     "rnafold - fasta": {
         "content": [
             [
-                "transcriptome.fasta.fold:md5,5f8a62d2119ffa8ae0907917c772af02"
+                [
+                    {
+
+                    },
+                    "transcriptome.fasta.fold:md5,5f8a62d2119ffa8ae0907917c772af02"
+                ]
             ],
             [
-                "versions.yml:md5,76ca9d956465e05df59c27f000276284"
+                [
+                    {
+
+                    },
+                    "versions.yml:md5,76ca9d956465e05df59c27f000276284"
+                ]
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-05-22T09:28:31.983790151"
+        "timestamp": "2024-05-22T16:52:19.507543"
     }
 }