From fbd31a43b54e59ff840ad14500d55e068f2676e1 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 22 Mar 2022 16:39:41 +0100
Subject: [PATCH] gffread: unzip input fasta
---
src/nf_modules/gffread/main.nf | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/src/nf_modules/gffread/main.nf b/src/nf_modules/gffread/main.nf
index e573adf1..a6316606 100644
--- a/src/nf_modules/gffread/main.nf
+++ b/src/nf_modules/gffread/main.nf
@@ -54,7 +54,8 @@ process spliced_cds {
file_prefix = file_id
}
"""
-gffread -x -M - -g ${fasta} ${gtf} \
+gzip -dc ${fasta} > ${fasta.simpleName}_un.fasta
+gffread -x -M - -g ${fasta.simpleName}_un.fasta ${gtf} \
> ${file_prefix}.fasta
"""
}
\ No newline at end of file
--
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