From 9db26e0482ad628da8b6029a5e4ede551d3fa568 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 22 Mar 2022 16:56:59 +0100
Subject: [PATCH] gffread: unzip gtf for spliced_cds process
---
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 a6316606..bc1c87e0 100644
--- a/src/nf_modules/gffread/main.nf
+++ b/src/nf_modules/gffread/main.nf
@@ -55,7 +55,8 @@ process spliced_cds {
}
"""
gzip -dc ${fasta} > ${fasta.simpleName}_un.fasta
-gffread -x -M - -g ${fasta.simpleName}_un.fasta ${gtf} \
+gzip -dc ${gtf} > ${gff.simpleName}_un.gtf
+gffread -x -M - -g ${fasta.simpleName}_un.fasta ${gff.simpleName}_un.gtf \
> ${file_prefix}.fasta
"""
}
\ No newline at end of file
--
GitLab