put only gubbins in if statement

Author: taranewman

main.nf

@@ -68,13 +68,14 @@ workflow {
 
 // Now, combine these channels in the desired order
 
+   ch_pipeline_prov = pipeline_provenance.out
+   ch_snippy_prov = snippy_core.out.provenance
+   ch_snp_sites_prov = snp_sites.out.provenance
+   ch_iqtree_prov = iqtree.out.provenance
+   ch_shiptv_prov = shiptv.out.provenance
+
   if (!params.skip_gubbins) {
-    ch_pipeline_prov = pipeline_provenance.out
-    ch_snippy_prov = snippy_core.out.provenance
     ch_gubbins_prov = gubbins.out.provenance
-    ch_snp_sites_prov = snp_sites.out.provenance
-    ch_iqtree_prov = iqtree.out.provenance
-    ch_shiptv_prov = shiptv.out.provenance
 
     ch_provenance = ch_pipeline_prov
     .concat(ch_snippy_prov)
@@ -85,12 +86,6 @@ workflow {
     .collect()
 
   } else {
-    ch_pipeline_prov = pipeline_provenance.out
-    ch_snippy_prov = snippy_core.out.provenance
-    ch_snp_sites_prov = snp_sites.out.provenance
-    ch_iqtree_prov = iqtree.out.provenance
-    ch_shiptv_prov = shiptv.out.provenance
-
     ch_provenance = ch_pipeline_prov
     .concat(ch_snippy_prov)
     .concat(ch_snp_sites_prov)