Merge pull request #36 from genomic-medicine-sweden/pangolin-typing-m…

…edaka Pangolin typing with medaka
genomic-medicine-sweden · Nov 9, 2021 · 496f421 · 496f421
2 parents 8dfe837 + 3682878
commit 496f421
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/workflows/articNcovNanopore.nf b/workflows/articNcovNanopore.nf
@@ -125,7 +125,8 @@ workflow sequenceAnalysisMedaka {
      collateSamples(qc.pass.map{ it[0] }
                            .join(articMinIONMedaka.out.consensus_fasta, by: 0)
                            .join(articRemoveUnmappedReads.out))
-
+
+     pangolinTyping(articMinIONMedaka.out.consensus_fasta)
 
      if (params.outCram) {
         bamToCram(articMinIONMedaka.out.ptrim.map{ it[0] }