From 87bbbe89b92cdeb31d844dbb770e1cd63e4c1e89 Mon Sep 17 00:00:00 2001
From: Emilio Palumbo <emiliopalumbo@gmail.com>
Date: Thu, 6 Oct 2022 15:03:47 +0200
Subject: [PATCH] Support gzipped genome in gem index process

---
 modules/gem.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/gem.nf b/modules/gem.nf
index 4124689..c516f4f 100644
--- a/modules/gem.nf
+++ b/modules/gem.nf
@@ -6,8 +6,9 @@ process indexing {
     file "genome_index.gem"
 
     script:
+    def cat = genome.name.endsWith('.gz') ? 'zcat' : 'cat'
     """
-    sed 's/ .*//' ${genome} > genome_processed.fa
+    ${cat} ${genome} | sed 's/ .*//' > genome_processed.fa
     gem-indexer -i genome_processed.fa \
                 -o genome_index \
                 -T ${task.cpus} \