From fb44f36f66de87b04e85ccae37d9aee62300a84b Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Wed, 16 Sep 2020 19:08:24 +0100
Subject: [PATCH] Update main.nf

---
 software/rsem/calculateexpression/main.nf | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/software/rsem/calculateexpression/main.nf b/software/rsem/calculateexpression/main.nf
index 527b3eb9..2df4849b 100644
--- a/software/rsem/calculateexpression/main.nf
+++ b/software/rsem/calculateexpression/main.nf
@@ -32,6 +32,13 @@ process RSEM_CALCULATEEXPRESSION {
     def software   = getSoftwareName(task.process)
     def ioptions   = initOptions(options)
     prefix         = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    
+    def strandedness = ''
+    if (meta.strandedness == 'forward') {
+        strandedness = '--strandedness forward'
+    } else if (meta.strandedness == 'reverse') {
+        strandedness = '--strandedness reverse'
+    }
     def paired_end = meta.single_end ? "" : "--paired-end"
     """
     INDEX=`find -L ./ -name "*.grp" | sed 's/.grp//'`
@@ -39,6 +46,7 @@ process RSEM_CALCULATEEXPRESSION {
         --num-threads $task.cpus \\
         --temporary-folder ./tmp/ \\
         $paired_end \\
+        $strandedness \\
         $ioptions.args \\
         $reads \\
         \$INDEX \\