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add check if mirgene_db_species is set if mirgene_db #315

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Feb 16, 2024
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add check if mirgene_db_species is set if mirgene_db #315

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1 change: 1 addition & 0 deletions workflows/smrnaseq.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,7 @@ if (!params.mirgenedb) {
if (params.mirgenedb_mature) { reference_mature = file(params.mirgenedb_mature, checkIfExists: true) } else { exit 1, "Mature miRNA fasta file not found: ${params.mirgenedb_mature}" }
if (params.mirgenedb_hairpin) { reference_hairpin = file(params.mirgenedb_hairpin, checkIfExists: true) } else { exit 1, "Hairpin miRNA fasta file not found: ${params.mirgenedb_hairpin}" }
if (params.mirgenedb_gff) { mirna_gtf = file(params.mirgenedb_gff, checkIfExists: true) } else { exit 1, "MirGeneDB gff file not found: ${params.mirgenedb_gff}"}
if (!params.mirgenedb_species) { exit 1, "MirGeneDB species not set, please specify via the --mirgenedb_species parameter"}
}

include { INPUT_CHECK } from '../subworkflows/local/input_check'
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