From 0ceb0fc5146cc6e943d74ffcfd1d075e871412b0 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 22 Mar 2022 11:13:55 +0100
Subject: [PATCH] gffread: simplify extract cds process
---
src/nf_modules/gffread/main.nf | 13 ++-----------
1 file changed, 2 insertions(+), 11 deletions(-)
diff --git a/src/nf_modules/gffread/main.nf b/src/nf_modules/gffread/main.nf
index 423697c0..e573adf1 100644
--- a/src/nf_modules/gffread/main.nf
+++ b/src/nf_modules/gffread/main.nf
@@ -54,16 +54,7 @@ process spliced_cds {
file_prefix = file_id
}
"""
-gffread -x -M - -g ${fasta} ${gtf} | \
-bioawk -c fastx '{ print \$name, \$seq }' | \
-while read line; \
-do \
-name=\$(echo \$line | cut -f 1); \
-echo \$line | cut -f 2 | \
-awk -F "" '{ for (i = 3; i <= NF; i += 3) \
-printf "%s%s", \$i, (i+3>NF?"\n":FS) }' | \
-awk -v name="\$name" '{ print ">"name; print \$1 }'; \
-done \
-> ${file_prefix}.fasta
+gffread -x -M - -g ${fasta} ${gtf} \
+ > ${file_prefix}.fasta
"""
}
\ No newline at end of file
--
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