#!/bin/bash -l
#$ -cwd
#$ -j y
#$ -P wax-dk
#$ -o log.txt
#$ -N bam2bw
#$ -pe omp 4
#$ -l mem_per_core=8G
#$ -l h_rt=04:00:00
# -l scratch_free=200G
 
echo "=========================================================="
Start_Time=$(date +"%s")
echo "Starting on : $(date)"
echo "Running on node   : $(hostname)"
echo "Current job ID    : $JOB_ID"
echo "Current job name  : $JOB_NAME"
echo "Task index number : $TASK_ID"
echo "=========================================================="

## example
## fd -e gz | xargs -n1 -I{} bash -c "zcat {} | wc -l"

module load miniconda
conda activate /projectnb/wax-es/routines/condaenv/deeptools

set -eu

# Forward strand
bamCoverage \
    -b unique_primary.bam \
    -o unique_primary.forward.bw \
    --filterRNAstrand forward \
    --normalizeUsing CPM \
    -p 4


# Reverse strand
bamCoverage \
    -b unique_primary.bam \
    -o unique_primary.reverse.bw \
    --filterRNAstrand reverse \
    --normalizeUsing CPM \
    -p 4

End_Time=$(date +"%s")
diff=$(($End_Time-$Start_Time))
echo "$(($diff / 3600)) hours, $((($diff / 60) % 60)) minutes and $(($diff % 60)) seconds elapsed."
echo "=========================================================="