1_JU28_59vs17_SNP_calling.sh: add training step analysis

src/1_JU28_59vs17_SNP_calling.sh

 #!/bin/sh
-./nextflow src/SNP_calling.nf -c src/SNP_calling.config -profile docker --fasta "data/fasta/DBG2OLC-output2.fasta" --fastq "data/fastq/*_{1,2}.fastq.gz" -resume -w ~/data/work/
+
+# generate training set
+ll *.gz | sed 's/.gz//g' | awk '{system("gunzip -c "$9".gz > ~/data/JU28_59vs17_SNP/data/samples/"$9)}'
+cd ~/data/JU28_59vs17_SNP/data/samples/
+~/scripts/fastq_sampler/fastq_sampler.py -i 100000 -f MR_350_clean_1.fastq -g MR_350_clean_2.fastq
+~/scripts/fastq_sampler/fastq_sampler.py -i 100000 -f MR_550_clean_1.fastq -g MR_550_clean_2.fastq
+~/scripts/fastq_sampler/fastq_sampler.py -i 100000 -f NG-10944_JU2859_bis_lib169352_5217_1_1.fastq -g NG-10944_JU2859_bis_lib169352_5217_1_2.fastq
+ll s_*.fastq | awk '{system("gzip < "$9" > "$9".gz")}'
+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\"]"
+~/scripts/sms.sh "SNP done"
+
+# real set analysis
+
+./nextflow src/SNP_calling.nf -c src/SNP_calling.config -profile docker --fasta "data/fasta/DBG2OLC-output2.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"
 
 ./nextflow src/SNP_calling.nf -c src/SNP_calling.config -profile docker --fasta "data/fasta/DBG2OLC-output2.fasta" --fastq "data/fastq/*_{1,2}.fastq.gz" --sam "results/mapping/sam/*.sam" -resume -w ~/data/work/
 
-./nextflow src/SNP_calling.nf -c src/SNP_calling.config -profile docker --fasta "data/fasta/DBG2OLC-output2.fasta" --fastq "data/fastq/*_{1,2}.fastq.gz" --sam "results/mapping/sam/*.sam" -resume -w ~/data/work/ --tumor "[\"NG-10944_JU2859_bis_lib169352_5217_1\"]" --normal "[\"MR_550_clean\"], \"MR_350_clean\"]"
+./nextflow src/SNP_calling.nf -c src/SNP_calling.config -profile docker --fasta "data/fasta/DBG2OLC-output2.fasta" --fastq "data/fastq/*_{1,2}.fastq.gz" --sam "results/mapping/sam/*.sam" -resume -w ~/data/work/ --tumor "[\"NG-10944_JU2859_bis_lib169352_5217_1\"]" --normal "[\"MR_550_clean\", \"MR_350_clean\"]"
+~/scripts/sms.sh "SNP done"
+
+