Update subworkflows/local/prepare_genome/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
nf-core · Oct 8, 2024 · acd40b2 · acd40b2
1 parent 24ea7ad
commit acd40b2
Showing 1 changed file with 1 addition and 1 deletion.
diff --git 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()