From a275f3a661b155fd75de560d8d4058c6d2d8b8cf Mon Sep 17 00:00:00 2001
From: MarieLataretu <52002068+MarieLataretu@users.noreply.github.com>
Date: Wed, 25 Sep 2024 15:35:03 +0200
Subject: [PATCH] using the primer-trimmed bam file as input for freyja

freyja expects a trimmed bam file, else mixed variants in primer regions mess up the lineage abundance estimation
---
 poreCov.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/poreCov.nf b/poreCov.nf
index fcb25cd..833e8c4 100755
--- a/poreCov.nf
+++ b/poreCov.nf
@@ -443,7 +443,7 @@ workflow {
                     read_screening_lsc_wf(filtered_reads_ch)
                 }
                 if (params.freyja) {
-                    read_screening_freyja_wf(artic_ncov_wf.out.binary_alignment.combine(reference_for_qc_input_ch))
+                    read_screening_freyja_wf(artic_ncov_wf.out.trimmed_bam.map{it -> [it[0], it[1]]}.combine(reference_for_qc_input_ch))
                 }
             }
             alignments_ch = align_to_reference(filtered_reads_ch.combine(reference_for_qc_input_ch))