From bee02e81ace740cc54310a6b1f878015668b6bdd Mon Sep 17 00:00:00 2001
From: khalid <khalid.belkhir@umontpellier.fr>
Date: Mon, 29 Nov 2021 17:49:49 +0100
Subject: [PATCH] remove empty first line from flye fasta assembly
---
tools/flye/flye.rule.snakefile | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/tools/flye/flye.rule.snakefile b/tools/flye/flye.rule.snakefile
index d57d5538..3f6d9848 100755
--- a/tools/flye/flye.rule.snakefile
+++ b/tools/flye/flye.rule.snakefile
@@ -20,5 +20,6 @@ rule <step_name>__flye:
"--out-dir {params.output_dir} "
"-t {threads} "
"{params.scaffold} {params.keep_haplotypes} |& tee {log} ;"
- "awk '/^>/ {{printf(\"\n%s\n\",$0);next; }} {{ printf(\"%s\",$0);}} END {{printf(\"\n\");}}' < {params.output_dir}/assembly.fasta > {params.output_dir}/assembly.fa; "
- "mv {params.output_dir}/assembly.fa > {params.output_dir}/assembly.fasta"
\ No newline at end of file
+ "awk '/^>/ {{printf(\"\\n%s\\n\",$0);next; }} {{ printf(\"%s\",$0);}} END {{printf(\"\\n\");}}' < {params.output_dir}/assembly.fasta > {params.output_dir}/assembly.fa; "
+ "tail -n +2 {params.output_dir}/assembly.fa > {params.output_dir}/assembly.fasta; "
+ "rm -f {params.output_dir}/assembly.fa"
\ No newline at end of file
--
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