Improve the WGS FASTQ management wizards

[Nicklas Nordborg]

Now that we have decided to actually keep the WGS FASTQ files on a backup server the "Restore FASTQ from alignment" functionality is probably not needed. Due to space restriction we still have to move FASTQ files to a backup server and it would be nice to have information about were are files are. The scanning wizard should be able to also check the backup server and if a FASTQ file exists in the backup it should be possible to delete it from the primary storage. The restore wizard should be able to restore from the backup server. Alternatively the alignment script should be able to directly pull the FASTQ files from the backup server (but this will be another ticket).

[Nicklas Nordborg]

In 7592:

References #1574: Improve the WGS FASTQ management wizards

Implemented support for scanning the backup server. Results from the wizard are now more detailed.

[Nicklas Nordborg]

In 7593:

References #1574: Improve the WGS FASTQ management wizards

Files that are found on both the primary and the backup server can now be removed from the primary server.

[Nicklas Nordborg]

In 7595:

References #1574: Improve the WGS FASTQ management wizards

Introduced a setting <backup-archive-dna> in reggie-config.xml that points to a read-only alternate location of WGS FASTQ files.

Changed the WGS alignment code to use FASTQ files from this location if they don't exist on the primary location. It has not been tested yet due to downtime of the cluster.

[Nicklas Nordborg]

In 7596:

References #1574: Improve the WGS FASTQ management wizards

Need to bind the backup folder also when starting the container.

[Nicklas Nordborg]

In 7597:

References #1574: Improve the WGS FASTQ management wizards

Added a check that the FASTQ files exists. This will normally be cathced by the 'cp' statement, but not when debugging since the zcat ... || true swallows that error and creates an empty file instead.

[Nicklas Nordborg]

In 7598:

References #1574: Improve the WGS FASTQ management wizards

Added support for restoring the FASTQ files from the backup server instead of from the alignment.