deduplicate by biosample AFTER mutation calling

Rachel Colquhoun · rmcolq · commit 191442d75cdd · 2021-02-08T09:10:20.000Z
diff --git a/workflows/process_cog_uk.nf b/workflows/process_cog_uk.nf
@@ -19,7 +19,7 @@ workflow process_cog_uk {
       preprocess_cog_uk(uk_fasta, uk_metadata, uk_accessions)
       pangolin_cog_uk(preprocess_cog_uk.out.fasta, preprocess_cog_uk.out.metadata)
       deduplicate_by_cogid_cog_uk(preprocess_cog_uk.out.fasta, pangolin_cog_uk.out.metadata)
-      align_and_variant_call_cog_uk(deduplicate_cog_uk.out.fasta)
+      align_and_variant_call_cog_uk(deduplicate_by_cogid_cog_uk.out.fasta)
       deduplicate_by_biosample_cog_uk(align_and_variant_call_cog_uk.out.fasta,deduplicate_by_cogid_cog_uk.out.metadata)
       filter_and_trim_cog_uk(deduplicate_by_biosample_cog_uk.out.fasta, deduplicate_by_biosample_cog_uk.out.metadata)
     emit:
