From 84da917bc464f02147a40515ebad4942880a4d2c Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Wed, 17 Jan 2024 20:53:29 +0000
Subject: [PATCH] Fixing the error :)

---
 subworkflows/local/umi_dedup.nf | 3 +--
 workflows/smrnaseq.nf           | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/subworkflows/local/umi_dedup.nf b/subworkflows/local/umi_dedup.nf
index 3d12fd99..4a7f80f9 100644
--- a/subworkflows/local/umi_dedup.nf
+++ b/subworkflows/local/umi_dedup.nf
@@ -24,11 +24,10 @@ workflow DEDUPLICATE_UMIS {
 
     if (!bt_index){
         INDEX_GENOME ( [ [:], fasta ] )
-        bt_index      = INDEX_GENOME.out.bowtie_indices
+        bt_index      = INDEX_GENOME.out.index
         fasta_formatted = INDEX_GENOME.out.fasta
         ch_versions     = ch_versions.mix(INDEX_GENOME.out.versions)
     } else {
-        bt_index     = Channel.fromPath("${bt_index}**ebwt", checkIfExists: true).ifEmpty { exit 1, "Bowtie1 index directory not found: ${bt_index}" }
         fasta_formatted = fasta
     }
 
diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf
index 872de5f3..02501098 100644
--- a/workflows/smrnaseq.nf
+++ b/workflows/smrnaseq.nf
@@ -166,7 +166,7 @@ workflow SMRNASEQ {
 
             DEDUPLICATE_UMIS (
                 fasta_ch,
-                INDEX_GENOME.out.bowtie_indices,
+                INDEX_GENOME.out.index,
                 FASTQ_FASTQC_UMITOOLS_FASTP.out.reads,
                 params.umi_stats
             )