1_JU28_59vs17_SNP_calling.sh: add analysis of final_assembly.fasta

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*"