Hi, I seem to have a problem getting my output in the right location. Using the following call..
workdir="$1"
files=($(awk '{print $1}' $2 ))
infile="$workdir"/bam/${files[$SGE_TASK_ID]}.sorted.dedup.bam
macs2 predictd -i $infile -f BAM -g mm -m 5 50 --outdir "$workdir"/macs2/qc --rfile ${$infile%.sorted.dedup.bam}_model.r
..my input goes to $workdir/bam
Any suggestions? Thanks!