make gubbins provenance optional

BCCDC-PHL · Dec 4, 2024 · 8c11990 · 8c11990
1 parent f603314
commit 8c11990
Showing 1 changed file with 13 additions and 1 deletion.
diff --git a/main.nf b/main.nf
@@ -73,14 +73,26 @@ workflow {
   ch_shiptv_prov = shiptv.out.provenance
 
 // Now, combine these channels in the desired order
-  ch_provenance = ch_pipeline_prov
+
+  if (!params.skip_gubbins) {
+    ch_provenance = ch_pipeline_prov
     .concat(ch_snippy_prov)
     .concat(ch_gubbins_prov)
     .concat(ch_snp_sites_prov)
     .concat(ch_iqtree_prov)
     .concat(ch_shiptv_prov)
     .collect()
 
+  } else {
+    ch_provenance = ch_pipeline_prov
+    .concat(ch_snippy_prov)
+    .concat(ch_snp_sites_prov)
+    .concat(ch_iqtree_prov)
+    .concat(ch_shiptv_prov)
+    .collect()
+  }
+
+
   collect_provenance(ch_provenance)
 
 }