From 3ed5a9ca887b7fdcc28c0dab9fc9a2aa15ff61f4 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 1 Oct 2021 11:46:32 +0200
Subject: [PATCH] emase-zero: fix gene_to_transcript file to add strain info to
gene name
---
src/nf_modules/emase-zero/main.nf | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/src/nf_modules/emase-zero/main.nf b/src/nf_modules/emase-zero/main.nf
index fac633c2..005bebc4 100644
--- a/src/nf_modules/emase-zero/main.nf
+++ b/src/nf_modules/emase-zero/main.nf
@@ -45,7 +45,9 @@ process emase {
script:
"""
grep ">" ${fasta} | sed 's/>//' > tr_list.txt
-grep -Fw -f tr_list.txt ${gene_to_transcript} > gene_to_transcript.txt
+grep -Fw -f tr_list.txt ${gene_to_transcript} | \
+ sed -E 's/(.+gn[0-9]+)(.+)(_.+)/\\1\\3\\2\\3/g' > \
+ gene_to_transcript.txt
emase-zero ${params.count} \
-o ${bin.simpleName}.quantified \
-l ${transcript_length} \
--
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