From 4aec8f0896623b1e8bf262ccb4051ac74a1e090b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Thu, 11 Oct 2018 11:26:54 +0200
Subject: [PATCH] 1_JU28_59vs17_SNP_calling.sh: add analysis of
final_assembly.fasta
---
src/1_JU28_59vs17_SNP_calling.sh | 9 +++++++++
1 file changed, 9 insertions(+)
diff --git a/src/1_JU28_59vs17_SNP_calling.sh b/src/1_JU28_59vs17_SNP_calling.sh
index 93de93b..415a58f 100644
--- a/src/1_JU28_59vs17_SNP_calling.sh
+++ b/src/1_JU28_59vs17_SNP_calling.sh
@@ -27,6 +27,15 @@ src/intersect_SNP.R \
data/list_of_enzymes.csv
~/scripts/sms.sh "SNP analysis done"
+./nextflow src/SNP_calling.nf -c src/SNP_calling.config -profile docker --fasta "data/fasta/final_assembly.fasta" --fastq "data/fastq/*_{1,2}.fastq.gz" -resume -w ~/data/work/ --tumor "[\"NG-10944_JU2859_bis_lib169352_5217_1\"]" --normal "[\"MR_550_clean\", \"MR_350_clean\"]"
+~/scripts/sms.sh "SNP done"
+src/intersect_SNP.R \
+ results/SNP/vcf_samtools/normal_sample_filtered.csv \
+ results/SNP/vcf_samtools/tumor_sample_filtered.csv \
+ results/fasta/DBG2OLC_output2_filtered.fasta \
+ data/list_of_enzymes.csv
+~/scripts/sms.sh "SNP analysis done"
+
# on the PSMN
find ~/data/ -name "MR_350_clean*"
--
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