So I solved this myself, it wasn't too tricky after all. Why not reinvent the wheel eh ?

Sambamba bash script

#!/bin/bash
# Check window coverage on Wochenende sorted dup.bam output

# Actually run for each BAM file
for i in *dup.bam; do
        input=$i
        sec_input=${input%%.bam}
        #sec_in_bam=${input%%.bam}

        window=150
        overlap=75
        covMax=999999999

        # Get coverage depth in windows
        # x threads, Windows 100000, overlap 50000, -c minimum coverage.
        # SLURM
        $scheduler $path_sambamba depth window -t $THREADS --max-coverage=$covMax --window-size=$window --overlap $overlap -c 10 ${sec_input}.bam > ${sec_input}_cov_window.txt &

done
wait

Followup awk script

cat awk_crispressoWGS_regions.sh

#/bin/bash
# Feb 2022, make regions for https://github.com/pinellolab/CRISPResso2 wgs

#example target format tab separated
#chr6 51002798 51002820 R2 NA NA NA
awk -F "\t" '{print $1 "\t" $2 "\t" $3 "\tR" FNR "\tNA" "\tNA" "\tNA"}' yourBAMfilename.trm.ns.fix.s.dup_cov_window.txt > tmp.txt

# remove header on line 1
grep -v "#" tmp.txt > WGS_regions.txt