diff --git a/modules/artic.nf b/modules/artic.nf index dd47eb94..1734eb8e 100644 --- a/modules/artic.nf +++ b/modules/artic.nf @@ -15,8 +15,8 @@ process artic { tuple val(sample), file(fastq), file(reference), file(bed) output: - tuple val(sample), file("artic/${sample}.primertrim.sorted.bam"), file("artic/${sample}.primertrim.sorted.bam.bai"), emit: bam - path "consensus/${sample}.consensus.fa", emit: consensus + tuple val(sample), file("artic/${sample}.primertrim.sorted.bam"), file("artic/${sample}.primertrim.sorted.bam.bai"), emit: bam, optional: true + path "consensus/${sample}.consensus.fa", emit: consensus, optional: true tuple val("artic"), env(artic_version), emit: artic_version path "artic/${sample}*" path "logs/${task.process}/${sample}.${workflow.sessionId}.log"