From a5a6973fcf161d0449b216c166ba232c6c55bcbb Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Sat, 21 May 2022 08:33:49 +0200
Subject: [PATCH] picard: make reference sequence optional

---
 modules/picard/collecthsmetrics/main.nf       | 2 +-
 modules/picard/collectmultiplemetrics/main.nf | 3 ++-
 modules/picard/collectwgsmetrics/main.nf      | 3 ++-
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/modules/picard/collecthsmetrics/main.nf b/modules/picard/collecthsmetrics/main.nf
index 317aff4b..06b6b8f3 100644
--- a/modules/picard/collecthsmetrics/main.nf
+++ b/modules/picard/collecthsmetrics/main.nf
@@ -24,7 +24,7 @@ process PICARD_COLLECTHSMETRICS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def reference = fasta ? "-R $fasta" : ""
+    def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
 
     def avail_mem = 3
     if (!task.memory) {
diff --git a/modules/picard/collectmultiplemetrics/main.nf b/modules/picard/collectmultiplemetrics/main.nf
index a653b549..3c3152df 100644
--- a/modules/picard/collectmultiplemetrics/main.nf
+++ b/modules/picard/collectmultiplemetrics/main.nf
@@ -22,6 +22,7 @@ process PICARD_COLLECTMULTIPLEMETRICS {
     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 CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -35,7 +36,7 @@ process PICARD_COLLECTMULTIPLEMETRICS {
         $args \\
         --INPUT $bam \\
         --OUTPUT ${prefix}.CollectMultipleMetrics \\
-        --REFERENCE_SEQUENCE $fasta
+        $reference
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf
index e6dd49e9..13446fcf 100644
--- a/modules/picard/collectwgsmetrics/main.nf
+++ b/modules/picard/collectwgsmetrics/main.nf
@@ -21,6 +21,7 @@ process PICARD_COLLECTWGSMETRICS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${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.'
@@ -34,7 +35,7 @@ process PICARD_COLLECTWGSMETRICS {
         $args \\
         --INPUT $bam \\
         --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
-        --REFERENCE_SEQUENCE $fasta
+        $reference
 
 
     cat <<-END_VERSIONS > versions.yml