From ce06694af8ca2f7453206aa974c2c9a2b99ec093 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Tue, 26 Jul 2022 21:51:47 +0100
Subject: [PATCH] Added support for ext.args in samtools/faidx (#1919)

ext.args was not used in the actual command-line

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/samtools/faidx/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/samtools/faidx/main.nf b/modules/samtools/faidx/main.nf
index fdce7d9b..11e688b3 100644
--- a/modules/samtools/faidx/main.nf
+++ b/modules/samtools/faidx/main.nf
@@ -22,6 +22,7 @@ process SAMTOOLS_FAIDX {
     """
     samtools \\
         faidx \\
+        $args \\
         $fasta
 
     cat <<-END_VERSIONS > versions.yml