00_build_index_hisat2.sh

#!/bin/bash
#if [ "$#" -ne 2 ] ; then
#echo "please provide:"
#echo -e "\t\t(1) name for index, preferably the NAM line name"
#echo -e "\t\t(2) genome sequences, use only scaffolds"
#echo "";
#echo "./00_build_index_hisat2 <NAM name> <FASTA-scaffolds-file>" ;
#echo "";
#exit 0;
#fi

NAM=$(basename $(dirname $(pwd)))
file=$1

module load hisat2
hisat2-build ${file} $NAM