Converted ch_bowtie_index to value channel

CHANGELOG.md

@@ -8,8 +8,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#481]](https://github.com/nf-core/smrnaseq/pull/481) - Fix [MIRTOP_STATS IndexError](https://github.com/nf-core/smrnaseq/issues/477) - Fix mirtop process execution when mirgenedb is used.
 - [[#482]](https://github.com/nf-core/smrnaseq/pull/482) - Update documentation regarding MirgeneDB input files.
 - [[#486]](https://github.com/nf-core/smrnaseq/pull/486) - Replace `CSVTK_JOIN` to improve processing in large amount of files.
-- [[#494]](https://github.com/nf-core/smrnaseq/pull/494) - Update [help text](https://github.com/nf-core/smrnaseq/issues/491) for `--fasta` parameter
 - [[#493]](https://github.com/nf-core/smrnaseq/pull/493) - Fix [[#488]](https://github.com/nf-core/smrnaseq/issues/488) - Fix runtime error that can occur when params.genome is set.
+- [[#494]](https://github.com/nf-core/smrnaseq/pull/494) - Update [help text](https://github.com/nf-core/smrnaseq/issues/491) for `--fasta` parameter.
+- [[#494]](https://github.com/nf-core/smrnaseq/pull/496) - Fix [bowtie_index channel](https://github.com/nf-core/smrnaseq/issues/496) when in dir format.
 
 ## v2.4.0 - 2024-10-14 - Navy Iron Boxer
 

workflows/smrnaseq.nf

@@ -211,7 +211,7 @@ workflow NFCORE_SMRNASEQ {
     genome_stats = Channel.empty()
     if (has_fasta){
         GENOME_QUANT (
-            ch_bowtie_index,
+            ch_bowtie_index.first(),
             ch_fasta,
             MIRNA_QUANT.out.unmapped
         )
@@ -232,7 +232,7 @@ workflow NFCORE_SMRNASEQ {
                 FASTQ_FIND_MIRNA_MIRDEEP2 (
                         ch_reads_for_mirna,
                         ch_fasta,
-                        ch_bowtie_index,
+                        ch_bowtie_index.first(),
                         ch_mature_hairpin,
                 )
         ch_versions = ch_versions.mix(FASTQ_FIND_MIRNA_MIRDEEP2.out.versions)