From e994f277ed0acfd038d7d6776e60ec68352f7a92 Mon Sep 17 00:00:00 2001
From: Yuk Kei Wan <ywan6@alumni.jh.edu>
Date: Mon, 9 Oct 2023 08:16:06 +0000
Subject: [PATCH] update

---
 subworkflows/local/align_graphmap2.nf | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/subworkflows/local/align_graphmap2.nf b/subworkflows/local/align_graphmap2.nf
index 551431be..27bae966 100644
--- a/subworkflows/local/align_graphmap2.nf
+++ b/subworkflows/local/align_graphmap2.nf
@@ -42,15 +42,12 @@ workflow ALIGN_GRAPHMAP2 {
 
     GRAPHMAP2_ALIGN ( ch_alignment_input, ch_reference, ch_reference_index )
     GRAPHMAP2_ALIGN.out.sam
-        .map { it -> [ it[0], it[1], [] ] }
+        .map { it -> [ it[0], it[1], it[1] ] }
         .set { ch_samtools_input }
-    ch_samtools_input
-        .map { it -> it[2] }
-        .set { ch_notneeded_fasta }
     ch_samtools_input
         .map { it -> it[2] }
         .set { ch_notneeded_qname }
-    SAMTOOLS_VIEW ( ch_samtools_input, ch_notneeded_fasta, ch_notneeded_qname )
+    SAMTOOLS_VIEW ( ch_samtools_input, ch_fasta, ch_notneeded_qname )
     SAMTOOLS_SORT ( SAMTOOLS_VIEW.out.bam )
     ch_sorted_bam = SAMTOOLS_SORT.out.bam
     SAMTOOLS_INDEX ( ch_sorted_bam )