I would like to get the bedgraphs generated by macs2. I tried adding -B and --bdg to the callpeaks command but it is failing. The parameters show up in the usage from macs2 itself but not in the ENCODE wrapper.
Edits I tried in encode_task_macs2_chip.py:
in parse_arguements:
parser.add_argument('--bdg', action='store_true', help='bedgraphs')
in macs2:
run_shell_cmd(
' macs2 callpeak '
'-t {ta} {ctl_param} -f BED -n {prefix} -g {gensz} -p {pval_thresh} '
'--nomodel --shift {shiftsize} --extsize {extsize} --keep-dup all --bdg --SPMR'.format(
ta=ta,
ctl_param='-c {ctl_ta}'.format(ctl_ta=ctl_ta) if ctl_ta else '',
prefix=prefix,
gensz=gensz,
pval_thresh=pval_thresh,
shiftsize=0,
extsize=fraglen,
)
)

The error I get:
ENCODE DCC MACS2 callpeak: error: unrecognized arguments: --bdg

What am I missing?
Thanks,
Belinda