From f31a8f3e97277769334a4ec309641f3b3a385cd3 Mon Sep 17 00:00:00 2001
From: Rachel LEGENDRE <rachel.legendre@pasteur.fr>
Date: Wed, 26 Jul 2023 10:31:52 +0200
Subject: [PATCH] fix typo error in paired end mode
---
workflow/rules/sortmerna.rules | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/workflow/rules/sortmerna.rules b/workflow/rules/sortmerna.rules
index 9fed2f6..3e384c6 100755
--- a/workflow/rules/sortmerna.rules
+++ b/workflow/rules/sortmerna.rules
@@ -70,10 +70,10 @@ rule sortmerna:
if [[ ${{#infiles[@]}} -eq 2 ]];
then
sortmerna --ref ${{fasta}} --idx-dir ${{idxdir}} --workdir {params.tmpdir}/{wildcards.SAMPLE} -threads {threads} --reads ${{infiles[0]}} --reads ${{infiles[1]}} --aligned out_paired_ribo --fastx --out2 --paired_out --other out_paired -v > {log.out} 2> {log.err}
- mv out_paired_fwd.fq${{ext}} {{outnorRNA[0]}}
- mv out_paired_rev.fq${{ext}} {{outnorRNA[1]}}
- mv out_paired_ribo_fwd.fq${{ext}} {{outrRNA[0]}}
- mv out_paired_ribo_rev.fq${{ext}} {{outrRNA[1]}}
+ mv out_paired_fwd.fq${{ext}} ${{outnorRNA[0]}}
+ mv out_paired_rev.fq${{ext}} ${{outnorRNA[1]}}
+ mv out_paired_ribo_fwd.fq${{ext}} ${{outrRNA[0]}}
+ mv out_paired_ribo_rev.fq${{ext}} ${{outrRNA[1]}}
#mv output.rRNA.log {log.out}
else
--
GitLab