From 0d30c10337d08063ae64ad1f8a4205542f49df0a Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 9 Jul 2021 15:46:56 +0200
Subject: [PATCH] gffread: remove empty line
---
src/nf_modules/gffread/main.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/nf_modules/gffread/main.nf b/src/nf_modules/gffread/main.nf
index 07e010e7..3f7a4db4 100644
--- a/src/nf_modules/gffread/main.nf
+++ b/src/nf_modules/gffread/main.nf
@@ -26,6 +26,6 @@ process gffread {
}
"""
gffread ${gtf} -g ${fasta} -M -x dup_${file_prefix}.fasta
- awk 'BEGIN {i = 1;} { if (\$1 ~ /^>/) { tmp = h[i]; h[i] = \$1; } else if (!a[\$1]) { s[i] = \$1; a[\$1] = "1"; i++; } else { h[i] = tmp; } } END { for (j = 1; j < i; j++) { print h[j]; print s[j]; } }' < dup_${file_prefix}.fasta > ${file_prefix}.fasta
+ awk 'BEGIN {i = 1;} { if (\$1 ~ /^>/) { tmp = h[i]; h[i] = \$1; } else if (!a[\$1]) { s[i] = \$1; a[\$1] = "1"; i++; } else { h[i] = tmp; } } END { for (j = 1; j < i; j++) { print h[j]; print s[j]; } }' < dup_${file_prefix}.fasta | grep -v -e "^\$" > ${file_prefix}.fasta
"""
}
--
GitLab