Preprocessing_Amulet_human

#!/bin/bash

samples=$(ls /home/scratch/yoshi/ | grep "[0-9][0-9]*.*")

# mkdir -p "amulet_output"

for lib in $samples; do
    echo "running sample $lib"
    # rm $lib/outs/possorted_bam.bam $lib/outs/possorted_bam.bam.bai
    mkdir -p "amulet_output/"$lib
    input_frag=$lib"/outs/fragments.tsv.gz"
    input_sc_csv=$lib"/outs/singlecell.csv"
    AMULET/AMULET.sh $input_frag $input_sc_csv AMULET/human_autosomes.txt AMULET/hg38-blacklist.v2.bed "amulet_output/"$lib AMULET &
    echo "completed "$lib
done