Add tidk optional

nf-core · Oct 29, 2024 · 25f9bbd · 25f9bbd
1 parent 05b062c
commit 25f9bbd
Show file tree

Hide file tree

Showing 3 changed files with 15 additions and 5 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -16,6 +16,9 @@ params {
     genome                     = null
     igenomes_base              = null
     igenomes_ignore            = false
+
+    // tidk skip
+    skip_tidk                  = false
     // Genome only option
     genome_only                = null
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -302,6 +302,12 @@
         "busco_config": {
           "type": "string",
           "description": "A path to a BUSCO config file (optional)"
+        },
+        "skip_tidk": {
+          "type": "boolean",
+          "description": "Do not run TIDK.",
+          "hidden": true,
+          "help_text": "You may wish to turn off the tidk subworkflow"
         }
       }
     }

diff --git a/workflows/genomeqc.nf b/workflows/genomeqc.nf
@@ -92,11 +92,12 @@ workflow GENOMEQC {
     //
     // Run TIDK
     //
-
-    FASTA_EXPLORE_SEARCH_PLOT_TIDK (
-        ch_fasta,
-        []
-    )
+    if (!params.skip_tidk) {
+        FASTA_EXPLORE_SEARCH_PLOT_TIDK (
+            ch_fasta,
+            []
+        )
+    }
 
     // Run genome only or genome + gff