From 36828787e5cf11d6f2c1f83024724da014a847ae Mon Sep 17 00:00:00 2001
From: henningonsbring <henning.onsbring@gmail.com>
Date: Thu, 4 Nov 2021 15:49:01 +0100
Subject: [PATCH] to allow pangolin typing with medaka

---
 workflows/articNcovNanopore.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/workflows/articNcovNanopore.nf b/workflows/articNcovNanopore.nf
index f6f15126..93f63e09 100644
--- 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] }