From 1fd19b76a386d7328bc91f440651db3aae8f8c2a Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 4 Oct 2021 17:05:59 +0200
Subject: [PATCH] emase-zero: remove personalized gene_to_transcript file
---
src/nf_modules/emase-zero/main.nf | 5 +----
1 file changed, 1 insertion(+), 4 deletions(-)
diff --git a/src/nf_modules/emase-zero/main.nf b/src/nf_modules/emase-zero/main.nf
index 4884f79e..87c5020d 100644
--- a/src/nf_modules/emase-zero/main.nf
+++ b/src/nf_modules/emase-zero/main.nf
@@ -45,13 +45,10 @@ process emase {
script:
"""
grep ">" ${fasta} | sed 's/>//' > tr_list.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} \
- -g gene_to_transcript.txt \
+ -g ${gene_to_transcript} \
${bin} &> ${file_id}_emase-zero_report.txt
"""
}
\ No newline at end of file
--
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