From 147563d68de698367f530850c9b79313004d6331 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 3 Oct 2018 18:42:41 +0200
Subject: [PATCH] 1_JU28_59vs17_SNP_calling.sh: fix tests cmd

---
 src/1_JU28_59vs17_SNP_calling.sh | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/1_JU28_59vs17_SNP_calling.sh b/src/1_JU28_59vs17_SNP_calling.sh
index 5937da1..d84081a 100644
--- a/src/1_JU28_59vs17_SNP_calling.sh
+++ b/src/1_JU28_59vs17_SNP_calling.sh
@@ -11,7 +11,9 @@ cd ~/projects/JU28_59vs17_SNP/
 
 # training set analysis
 
-./nextflow src/SNP_calling.nf -c src/SNP_calling.config -profile docker --fasta "data/fasta/DBG2OLC-output2.fasta" --fastq "data/samples/*_{1,2}.fastq.gz" -resume -w ~/data/work/ --tumor "[\"NG-10944_JU2859_bis_lib169352_5217_1\"]" --normal "[\"MR_550_clean\", \"MR_350_clean\"]"
+mkdir tests
+cd tests
+../nextflow ../src/SNP_calling.nf -c ../src/SNP_calling.config -profile docker --fasta "../data/fasta/DBG2OLC-output2.fasta" --fastq "../data/samples/*_{1,2}.fastq.gz" -resume -w ~/data/work_s/ --tumor "[\"s_NG-10944_JU2859_bis_lib169352_5217_1\"]" --normal "[\"s_MR_550_clean\", \"s_MR_350_clean\"]"
 ~/scripts/sms.sh "SNP done"
 
 # real set analysis
-- 
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