use -p option for mkdir

[soichih]

To allow for rerunning the failed job, we should use -p option for mkdir.

+ mkdir cortexmap ./cortexmap/cortexmap/
mkdir: cannot create directory 'cortexmap': File exists
mkdir: cannot create directory './cortexmap/cortexmap/': File exists

[soichih]

Also..

When a file from the staging job is copied to a local workdir, it should use "install" command instead of "cp". The staging jobs are write only, so when it's copied to workdir, the file attribute is retained and create read-only file. If a job is restarted, it will fail overwrite already copied file as it is set to read-only.

+ cp -v ../6079b5040a3c71d10084c850/6057a06d73b69e76f551d498/map.nii.gz ./metric/myelinmap.nii.gz
'../6079b5040a3c71d10084c850/6057a06d73b69e76f551d498/map.nii.gz' -> './metric/myelinmap.nii.gz'
cp: cannot create regular file './metric/myelinmap.nii.gz': Permission denied

To prevent this, you can simply use install command

[soichih]

I just patched this on v1.2-snr-input branch. I am not sure if there are any other branch that I should touch though.

fc9b3d9