From 1cda72fe39d9ff181ed7c39b6c2efb74ac831836 Mon Sep 17 00:00:00 2001
From: Erin Young <erin.olde@gmail.com>
Date: Tue, 26 Sep 2023 17:51:47 -0600
Subject: [PATCH] optional files

---
 modules/artic.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/artic.nf b/modules/artic.nf
index dd47eb9..1734eb8 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"