From acd40b23b6b5918b9ae4d44b9031d0ef41aed0b6 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Tue, 8 Oct 2024 08:14:18 +0200 Subject: [PATCH] Update subworkflows/local/prepare_genome/main.nf Co-authored-by: James A. Fellows Yates --- subworkflows/local/prepare_genome/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index 2f3f34b7..eba1d33c 100644 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -60,7 +60,7 @@ workflow PREPARE_GENOME { bool_has_fasta = val_fasta ? true : false ch_mirtrace_species = val_mirtrace_species ? Channel.value(val_mirtrace_species) : Channel.empty() - mirna_gtf_from_species = val_mirtrace_species ? (val_mirtrace_species == 'hsa' ? "https://raw.githubusercontent.com/nf-core/test-datasets/smrnaseq/reference/hsa.gff3" : "https://mirbase.org/download/CURRENT/genomes/${val_mirtrace_species}.gff3") : false + mirna_gtf_from_species = val_mirtrace_species ? (val_mirtrace_species == 'hsa' ? params.hsa_ref : "https://mirbase.org/download/CURRENT/genomes/${val_mirtrace_species}.gff3") : false ch_mirna_gtf = val_mirna_gtf ? Channel.fromPath(val_mirna_gtf, checkIfExists: true).map{ it -> [ [id:it.baseName], it ] }.collect() : ( mirna_gtf_from_species ? Channel.fromPath(mirna_gtf_from_species, checkIfExists: true).map{ it -> [ [id:it.baseName], it ] }.collect() : Channel.empty() ) ch_mirna_adapters = params.with_umi ? [] : Channel.fromPath(val_fastp_known_mirna_adapters, checkIfExists: true).collect()