From 97982e7c297267301aa5c8f78831e9392c9288e3 Mon Sep 17 00:00:00 2001 From: nschcolnicov Date: Tue, 7 Jan 2025 19:31:58 +0000 Subject: [PATCH] Converted ch_bowtie_index to value channel --- CHANGELOG.md | 3 ++- workflows/smrnaseq.nf | 4 ++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1ade665a..0c255771 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf index d7161c9b..fbd3aed2 100644 --- a/workflows/smrnaseq.nf +++ b/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)