Handling extraexons

biocorecrg · Nov 27, 2024 · 3dcc801 · 3dcc801
1 parent 3a991bf
commit 3dcc801
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Showing 3 changed files with 12 additions and 7 deletions.
diff --git a/modules/local/exorthist/generate_annotations.nf b/modules/local/exorthist/generate_annotations.nf
@@ -4,8 +4,7 @@ process GENERATE_ANNOTATIONS {
     label 'publish'
 
     input:
-    tuple val(genomeid), path(genome), path(annotation)
-    path extraexons
+    tuple val(genomeid), path(genome), path(annotation), path(extraexons)
 
     output:
     tuple val(genomeid), path("${genomeid}"), emit: idfolders

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -132,7 +132,7 @@
         "extraexons": {
           "type": "string",
           "description": "Extra exons (e.g. from VastDB)",
-          "format": "file-path"
+          "format": "file-path-pattern"
         },
         "bonafide_pairs": {
           "type": "string",

diff --git a/subworkflows/local/exorthist/prepare.nf b/subworkflows/local/exorthist/prepare.nf
@@ -56,14 +56,20 @@ workflow PREPARE {
 
     // We join channels. If no extraexons, then it's empty, so no problem
     data_to_annotation = genomes.join(annotations)
-    // TODO: To check what's goiing on here - check extraexons_ch
-    // data_to_annotation = data_to_annotation.join(extraexons_ch, remainder: true)
+
+    // print("EXTRAEXONS")
 
     if (extraexons) {
-        GENERATE_ANNOTATIONS(data_to_annotation, extraexons_ch)
+        data_to_annotation = data_to_annotation.join(extraexons_ch, remainder: true)
+        // data_to_annotation.view()
+        GENERATE_ANNOTATIONS(data_to_annotation)
     } else {
         // Sic: https://nextflow-io.github.io/patterns/optional-input/
-        GENERATE_ANNOTATIONS(data_to_annotation, Channel.fromPath("/path/to/NO_FILE").collect())
+        data_to_annotation.map { entry ->
+            entry.add(['/path/to/NO_FILE'])
+        }
+        data_to_annotation.view()
+        GENERATE_ANNOTATIONS(data_to_annotation)
     }
 
     clusters_split_ch = GENERATE_ANNOTATIONS.out.idfolders.toList().map{ [it, it].combinations().findAll{ a, b -> a[0] < b[0]} }