From 440a6f45a1f7bbe7822daed7ae6404c8da365712 Mon Sep 17 00:00:00 2001
From: Marc Hoeppner <mphoeppner@gmail.com>
Date: Tue, 10 Sep 2024 08:03:19 +0200
Subject: [PATCH] Fixing input channels for coverage calculation

---
 workflows/gabi.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/workflows/gabi.nf b/workflows/gabi.nf
index 3c46b7c..796f024 100644
--- a/workflows/gabi.nf
+++ b/workflows/gabi.nf
@@ -214,9 +214,9 @@ workflow GABI {
     */
     COVERAGE(
         ch_assemblies_clean,
-        ch_short_reads_only,
-        ch_ont_reads_only,
-        ch_pb_reads_only
+        ch_illumina_trimmed,
+        ch_ont_trimmed,
+        ch_pacbio_trimmed
     )
     ch_versions   = ch_versions.mix(COVERAGE.out.versions)
     ch_multiqc_illumina = ch_multiqc_illumina.mix(