Merge pull request #21 from BCCDC-PHL/skip-gubbins-in-provenance

make gubbins provenance optional
BCCDC-PHL · Dec 4, 2024 · 7cb06d4 · 7cb06d4
2 parents f603314 + 1f08fa6
commit 7cb06d4
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Showing 2 changed files with 14 additions and 2 deletions.
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)
 
 }
diff --git a/nextflow.config b/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = "BCCDC-PHL/snippy-core-phylogenomics"
   mainScript = 'main.nf'
   nextflowVersion = '>=20.01.0'
-  version= '0.1.2'
+  version= '0.1.3'
 }
 
 params {