Some folders for external samples are not changed to the specified group

[Nicklas Nordborg]

The possibility to set a specific group on files and folders created in the secondary analysis for external samples was introduced in #1174.

This functionality works by creating files and folders as normal with restricted access. In the final steps a 'chgrp' command is used to change files and folders to the specified group. A bug in this functionality causes some folders to be missed. This typically happens in the demux scripts which typically create a sub-folder within a folder and then only the sub-folder (and the files in it) get the correct group.

For example, prefix NN has bee configured to nngroup and we have a RNA sample with name NN_ABC123:

# Create directories 'ABC123' and 'lib.g'
mkdir -p <...>/external/NN/ABC123/lib.g

# Change group on the 'lib.g'
chgrp -R nngroup <...>/external/NN/ABC123/lib.g 

The ABC123 directory is left with the default group. We need to add 'chgrp' command for it to (without the -R flag).

It is expected that the NN directory already exists and that is has been configured by the server administrator.

[Nicklas Nordborg]

In 5930:

Fixes #1241: Some folders for external samples are not changed to the specified group