#viadastra Tutorial is here: python3 main.py -h

1. create config file and meta
   meta must contain columns: ['BAM', 'ID','path']
2. manage env

conda env create -f viadastra/viadastra_env.yml

2. make soft links

python3 main.py -c viadastra/configs/config.cfg -s 1

2. snp calling for all files

python3 main.py -c viadastra/configs/config.cfg -s 4

or

parallel -j 4 python viadastra/steps/step2_snp_calling.py viadastra/configs/config.cfg :::: logs/processing_list ;  curl -s -X POST https://api.telegram.org/bot1992203014:AAGXCU5ta31M-R10axejbBtxRJd0L1PNOow/sendMessage -d chat_id=639261746 -d text="snp calling выполнен"

3. filtrate pull and sort