From d5cacb230b7c8e1be08c13a56c0e1d6fa6813105 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 6 Oct 2021 15:35:54 +0200
Subject: [PATCH] samtools: add gzip for samtools faidx
---
src/nf_modules/samtools/main.nf | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index 4228dc5f..1a402ba5 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -18,7 +18,13 @@ process index_fasta {
script:
"""
-samtools faidx ${params.index_fasta} ${fasta}
+if gzip -t file.gz; then
+ zcat ${fasta} > ${fasta.simpleName}.fasta
+ samtools faidx ${params.index_fasta} ${fasta.simpleName}.fasta
+else
+ samtools faidx ${params.index_fasta} ${fasta}
+fi
+
"""
}
--
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