From c390385cf5a234906a30f013ba0a3c9a27b1b601 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Sun, 22 May 2022 06:44:05 +0200
Subject: [PATCH] revert wgsmetrics'

---
 modules/picard/collectwgsmetrics/main.nf | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf
index 13446fcf..cab1fe0c 100644
--- a/modules/picard/collectwgsmetrics/main.nf
+++ b/modules/picard/collectwgsmetrics/main.nf
@@ -21,7 +21,6 @@ process PICARD_COLLECTWGSMETRICS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
     def avail_mem = 3
     if (!task.memory) {
         log.info '[Picard CollectWgsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -35,7 +34,7 @@ process PICARD_COLLECTWGSMETRICS {
         $args \\
         --INPUT $bam \\
         --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
-        $reference
+        --REFERENCE_SEQUENCE ${fasta}
 
 
     cat <<-END_VERSIONS > versions.yml