feat: flag for busco

slsevilla · Mar 28, 2024 · 320cb64 · 320cb64
1 parent 0129b41
commit 320cb64
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Showing 2 changed files with 5 additions and 1 deletion.
diff --git a/nextflow.config b/nextflow.config
@@ -16,6 +16,10 @@ params {
     busco_db_path               = null
     coverage                    = 30 // can only increase above 30
 
+    // Run flags
+    run_busco                   = false
+
+
     // Additional input parameters for -entry SCAFFOLDS and CDC_SCAFFOLDS
     indir                       = null
     scaffolds_ext               = '.scaffolds.fa.gz'

diff --git a/workflows/phoenix.nf b/workflows/phoenix.nf
@@ -121,7 +121,7 @@ workflow PHOENIX_EXTERNAL {
 
         //fairy compressed file corruption check & generate read stats
         CORRUPTION_CHECK (
-            INPUT_CHECK.out.reads, false // true says busco is being run in this workflow
+            INPUT_CHECK.out.reads, params.run_busco
         )
         ch_versions = ch_versions.mix(CORRUPTION_CHECK.out.versions)