From 05ba4d901db380c6def3bc242ab18a2d88b25819 Mon Sep 17 00:00:00 2001
From: Subazini TK <subazinitk@gmail.com>
Date: Tue, 11 Jan 2022 22:39:21 +0100
Subject: [PATCH] samtools subsampling (#1194)

Co-authored-by: Subazini Thankaswamy Kosalai <sth036@orcus.orebroll.se>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/samtools/view/main.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/samtools/view/main.nf b/modules/samtools/view/main.nf
index fb31f70b..cb205d0b 100644
--- a/modules/samtools/view/main.nf
+++ b/modules/samtools/view/main.nf
@@ -18,6 +18,7 @@ process SAMTOOLS_VIEW {
 
     script:
     def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def reference = fasta ? "--reference ${fasta} -C" : ""
     def file_type = input.getExtension()
@@ -29,6 +30,7 @@ process SAMTOOLS_VIEW {
         ${reference} \\
         $args \\
         $input \\
+        $args2 \\
         > ${prefix}.${file_type}
 
     cat <<-END_VERSIONS > versions.yml