Parallel process multiple commands chromosome wise on swiss army knife
I am trying to extract SNPs from UK Biobank genotyping data.
For this, I am using swiss army knife on a for loop:
for i in {1..22}
do
dx run swiss-army-knife -icmd="bgenix -g ukb22828_c${i}_b0_v3.bgen -incl-rsids rsid.txt > chr${i}.bgen" -iin="$imp_file_dir/ukb22828_c${i}_b0_v3.bgen" -iin="$imp_file_dir/ukb22828_c${i}_b0_v3.bgen.bgi" -iin="$output/rsid.txt" --destination "$output/" --instance-type "mem1_ssd1_v2_x16"
done
This creates multiple instances. If I want to process them parallelly like using a workflow on the UI platform, how should I do it? 
Comments
1 comment
Hi the install instructions for Bgenix is here: https://enkre.net/cgi-bin/code/bgen/dir?ci=trunk
After that you can just use a parallelised script
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