Separate project archive folder for external samples

[Nicklas Nordborg]

The library preparation/sequencing wizards have support for processing external samples (RNA). In the end data files from the sequencing (FASTQ, etc) end up in the 'scanb' project archive folder. This is currently configured in the <project-archive> setting in the reggie-config.xml file and in the ProjectArchive fileserver item in BASE.

Since we are already generating different subfolder structures for regular and external samples it should not be too difficult to add settings for an 'external project archive'. Basically we need another configuration setting in the XML file (<external-project-archive>) and one more fileserver item (ExternalProjectArchive).

For external samples with an underscore in the name the characters before the underscore should be used as the name of the top-most folder inside the external project archive. External samples without an underscore doesn't have the extra folder. For example:

• AA_FOO is stored in <external-archive>/AA/AA_FOO
• AA_BAR is stored in <external-archive>/AA/AA_BAR
• BB_XYZ is stored in <external-archive>/BB/BB_XYZ
• MYSAMPLE is stored in <external-archive>/MYSAMPLE

The folder structure is repeated in the BASE server file structure, but instead of using /home/SCANB/SecondaryAnalysis as the main directory, /home/External/SecondaryAnalysis should be used.

Already existing information have to be fixed so that it is compatible with the new scheme. Some things may be possible to do with batch importers, some things may have to be done manually. The details about this should be documented in a special update notes wiki page.