Merge pull request #23 from BCCDC-PHL/update-snippy-provenance

make gubbins flexible

main.nf

@@ -65,16 +65,18 @@ workflow {
   // The basic idea is to build up a channel with the following structure:
   // [provenance_file_1.yml, provenance_file_2.yml, provenance_file_3.yml...]]
   // ...and then concatenate them all together in the 'collect_provenance' process.
-  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
 
-// 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
+
+// Add gubbins output if applicable and combine these channels in the desired order
 
   if (!params.skip_gubbins) {
+    ch_gubbins_prov = gubbins.out.provenance
+
     ch_provenance = ch_pipeline_prov
     .concat(ch_snippy_prov)
     .concat(ch_gubbins_prov)