diff --git a/workflows/ampliseq.nf b/workflows/ampliseq.nf index eec27d62..8d5afed3 100644 --- a/workflows/ampliseq.nf +++ b/workflows/ampliseq.nf @@ -122,16 +122,16 @@ tax_agglom_max = params.tax_agglom_max //use custom taxlevels from --dada_assign_taxlevels or database specific taxlevels if specified in conf/ref_databases.config if ( params.dada_ref_taxonomy ) { taxlevels = params.dada_assign_taxlevels ? "${params.dada_assign_taxlevels}" : - params.dada_ref_databases.containsKey(params.dada_ref_taxonomy) && params.dada_ref_databases[params.dada_ref_taxonomy]["taxlevels"] ?: "" + params.dada_ref_databases.containsKey(params.dada_ref_taxonomy) && params.dada_ref_databases[params.dada_ref_taxonomy]["taxlevels"] ? params.dada_ref_databases[params.dada_ref_taxonomy]["taxlevels"] : "" } else { taxlevels = params.dada_assign_taxlevels ? "${params.dada_assign_taxlevels}" : "" } if ( params.sintax_ref_taxonomy ) { - sintax_taxlevels = params.sintax_ref_databases.containsKey(params.sintax_ref_taxonomy) && params.sintax_ref_databases[params.sintax_ref_taxonomy]["taxlevels"] ?: "" + sintax_taxlevels = params.sintax_ref_databases.containsKey(params.sintax_ref_taxonomy) && params.sintax_ref_databases[params.sintax_ref_taxonomy]["taxlevels"] ? params.sintax_ref_databases[params.sintax_ref_taxonomy]["taxlevels"] : "" } else { sintax_taxlevels = "" } if ( params.kraken2_ref_taxonomy ) { kraken2_taxlevels = params.kraken2_assign_taxlevels ? "${params.kraken2_assign_taxlevels}" : - params.kraken2_ref_databases.containsKey(params.kraken2_ref_taxonomy) && params.kraken2_ref_databases[params.kraken2_ref_taxonomy]["taxlevels"] ?: "" + params.kraken2_ref_databases.containsKey(params.kraken2_ref_taxonomy) && params.kraken2_ref_databases[params.kraken2_ref_taxonomy]["taxlevels"] ? params.kraken2_ref_databases[params.kraken2_ref_taxonomy]["taxlevels"] : "" } else { kraken2_taxlevels = params.kraken2_assign_taxlevels ? "${params.kraken2_assign_taxlevels}" : "" } //make sure that taxlevels adheres to requirements when mixed with addSpecies