From fafae110686b9b2b5cea86b1d6682110105de0b1 Mon Sep 17 00:00:00 2001
From: "Maxime U. Garcia" <max.u.garcia@gmail.com>
Date: Fri, 11 Feb 2022 16:07:52 +0100
Subject: [PATCH] feat: nicer syntax (#1286)

* feat: nicer syntax

* feat: code polishing

* feat: code polishing
---
 modules/manta/germline/main.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/manta/germline/main.nf b/modules/manta/germline/main.nf
index 664085c5..5ddba51b 100644
--- a/modules/manta/germline/main.nf
+++ b/modules/manta/germline/main.nf
@@ -29,10 +29,11 @@ process MANTA_GERMLINE {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def input_files = input.collect{"--bam ${it}"}.join(' ')
     def options_manta = target_bed ? "--callRegions $target_bed" : ""
     """
     configManta.py \
-        --bam ${input.join(' --bam ')} \
+        ${input_files} \
         --reference $fasta \
         --runDir manta \
         $options_manta \