diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf index 90f1200dc7a..31fd2bb8594 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -16,7 +16,7 @@ process GATK4_GENOMICSDBIMPORT { output: tuple val(meta), path("$prefix") , optional:true, emit: genomicsdb tuple val(meta), path("$updated_db") , optional:true, emit: updatedb - tuple val(meta), path("*.interval_list"), optional:true, emit: intervallist + tuple val(meta), path("$interval_list"), optional:true, emit: intervallist path "versions.yml" , emit: versions when: @@ -45,6 +45,7 @@ process GATK4_GENOMICSDBIMPORT { interval_command = '' updated_db = "${wspace}" } + interval_list = interval_file ? interval_file : "${prefix}.interval_list" def avail_mem = 3072 if (!task.memory) {