From dea644353d0056461f41a8f1955e817039ddc041 Mon Sep 17 00:00:00 2001
From: Jens Preussner <jens.preussner@mpi-bn.mpg.de>
Date: Thu, 26 Apr 2018 10:50:11 +0200
Subject: [PATCH] Added flexibility for gz/plain reference fasta files

---
 src/reference.snake | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/reference.snake b/src/reference.snake
index a2e826a..f88a161 100644
--- a/src/reference.snake
+++ b/src/reference.snake
@@ -20,7 +20,7 @@ rule reference_download:
     'Downloading gencode transcriptome reference.'
   shell:
     """
-    zcat {input} > {output}
+    zcat -f {input} > {output}
     """
 
 if 'spikeIns' in config.get('reference', {}):
@@ -35,7 +35,7 @@ if 'spikeIns' in config.get('reference', {}):
       'Adding spike-in sequences to gencode transcriptome reference'
     shell:
       """
-      cat {input.ref} {input.spike} > {output}
+      zcat -f {input.ref} {input.spike} > {output}
       """
 
 rule tx2gene_from_fasta: