From bf0e0d857d516e62d25fd8da821dea0fd5576fe6 Mon Sep 17 00:00:00 2001
From: phue <patrick.huether@gmail.com>
Date: Sat, 20 Feb 2021 13:12:43 +0100
Subject: [PATCH] bwameth/align: fix fasta name retrieval

apparently bwameth doesn't like './' in front of the filepath? I have no idea. This works however
---
 software/bwameth/align/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/software/bwameth/align/main.nf b/software/bwameth/align/main.nf
index 14ac1b0b..4660e13a 100644
--- a/software/bwameth/align/main.nf
+++ b/software/bwameth/align/main.nf
@@ -31,7 +31,7 @@ process BWAMETH_ALIGN {
     def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
     """
-    INDEX=`find -L ./ -name "*bwameth.c2t" | sed 's/.bwameth.c2t//'`
+    INDEX=`find -L ${index} -name "*.bwameth.c2t" | sed 's/.bwameth.c2t//'`
 
     bwameth.py \\
         $options.args \\