diff --git a/src/1_JU28_59vs17_SNP_calling.sh b/src/1_JU28_59vs17_SNP_calling.sh index d84081a21c87a29e544e0c52178dddb7077b3be7..d806b325d9df67c6600287c1d1a09264fdcd0006 100644 --- a/src/1_JU28_59vs17_SNP_calling.sh +++ b/src/1_JU28_59vs17_SNP_calling.sh @@ -13,12 +13,12 @@ cd ~/projects/JU28_59vs17_SNP/ 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\"]" +../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\"]" --seq_number 800000 ~/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\"]" +./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/