Fixed linting and updated snapshot

nf-core · Nov 24, 2024 · 5265979 · 5265979
1 parent 3e549a2
commit 5265979
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Showing 3 changed files with 32 additions and 7 deletions.
diff --git a/subworkflows/nf-core/fasta_gxf_busco_plot/main.nf b/subworkflows/nf-core/fasta_gxf_busco_plot/main.nf
@@ -159,14 +159,14 @@ workflow FASTA_GXF_BUSCO_PLOT {
     assembly_batch_summary                      = ch_assembly_batch_summary             // channel: [ meta3, txt ]; meta3 ~ meta + [ val(mode), val(lineage) ]
     assembly_short_summaries_txt                = ch_assembly_short_summaries_txt       // channel: [ meta3, txt ]
     assembly_short_summaries_json               = ch_assembly_short_summaries_json      // channel: [ meta3, json ]
+    assembly_full_table                         = ch_assembly_full_table                // channel: [ meta3, tsv ]
     assembly_plot_summary_txt                   = ch_assembly_plot_summary              // channel: [ text ]
-    assembly_full_table                                  = ch_assembly_full_table                      // channel: [ meta3, tsv ]
     assembly_png                                = ch_assembly_png                       // channel: [ png ]
     annotation_batch_summary                    = ch_annotation_batch_summary           // channel: [ meta3, txt ]
     annotation_short_summaries_txt              = ch_annotation_short_summaries_txt     // channel: [ meta3, txt ]
     annotation_short_summaries_json             = ch_annotation_short_summaries_json    // channel: [ meta3, json ]
+    annotation_full_table                       = ch_annotation_full_table              // channel: [ meta3, tsv ]
     annotation_plot_summary_txt                 = ch_annotation_plot_summary            // channel: [ txt ]
-    annotation_full_table                               = ch_annotation_full_table                     // channel: [ meta3, tsv ]
     annotation_png                              = ch_annotation_png                     // channel: [ png ]
     versions                                    = ch_versions                           // channel: [ versions.yml ]
 }
diff --git a/subworkflows/nf-core/fasta_gxf_busco_plot/meta.yml b/subworkflows/nf-core/fasta_gxf_busco_plot/meta.yml
@@ -64,6 +64,12 @@ output:
         Channel containing BUSCO short summaries corresponding to fasta files
         Structure: [ val(meta), json ]
       pattern: "*.json"
+  - assembly_full_table:
+      description: |
+        Channel containing complete results in a tabular format with scores and lengths of BUSCO matches,
+        and coordinates (for genome mode) or gene/protein IDs (for transcriptome or protein modes)
+        Structure: [ val(meta), tsv ]
+      pattern: "*.tsv"
   - assembly_plot_summary_txt:
       type: file
       description: |
@@ -94,6 +100,12 @@ output:
         Channel containing BUSCO short summaries corresponding to annotation files
         Structure: [ val(meta), json ]
       pattern: "*.json"
+  - annotation_full_table:
+      description: |
+        Channel containing complete results in a tabular format with scores and lengths of BUSCO matches,
+        protein IDs in protein mode
+        Structure: [ val(meta), tsv ]
+      pattern: "*.tsv"
   - annotation_plot_summary_txt:
       type: file
       description: |
@@ -116,3 +128,4 @@ authors:
   - "@GallVp"
 maintainers:
   - "@GallVp"
+  - "@FernandoDuarteF"
diff --git a/subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test.snap b/subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test.snap
@@ -40,6 +40,12 @@
 
                 ],
                 "10": [
+
+                ],
+                "11": [
+
+                ],
+                "12": [
                     "versions.yml:md5,36b11c442943567e471af0abd474a10b",
                     "versions.yml:md5,9435355f913e283f60b4fb7ef77dd52a",
                     "versions.yml:md5,e9d65e2f2f13175e99c5b7f4ae1013b9"
@@ -54,6 +60,9 @@
 
                 ],
                 "5": [
+
+                ],
+                "6": [
                     [
                         {
                             "id": "test",
@@ -70,9 +79,6 @@
                         },
                         "test-bacteria_odb10-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
-                ],
-                "6": [
-
                 ],
                 "7": [
 
@@ -100,6 +106,9 @@
                         },
                         "test-bacteria_odb10-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
+                ],
+                "annotation_full_table": [
+
                 ],
                 "annotation_plot_summary_txt": [
 
@@ -146,6 +155,9 @@
                         },
                         "test2-bacteria_odb10-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
+                ],
+                "assembly_full_table": [
+
                 ],
                 "assembly_plot_summary_txt": [
 
@@ -168,9 +180,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-20T14:04:28.17169"
+        "timestamp": "2024-11-25T10:31:03.980517"
     },
     "candidatus_portiera_aleyrodidarum - bacteroides_fragilis - genome": {
         "content": [