Detect tiles with empty barcode files

[Nicklas Nordborg]

The first step when demuxing is to call picard ExtractIlluminaBarcodes which creates a directory with one file per tile containing barcodes for the reads on that tile.

Due to a hardware failure we got some corrupt sequencing data files that causes picard to create 0-sized barcode files for some tiles. This causes picard to crash in the next step (IlluminaBasecallsToFastq) but we think we can fix that so that picard simly ignore the tiles with no barcodes.

When this has been fixed we would also like to be able to track the tiles that has been ignored due to this. A warning should be recorded for the demux if more than 10 tiles/lane are skipped.

[Nicklas Nordborg]

(In [3140]) Fixes #742: Detect tiles with empty barcode files

The demux script now performs a check for 0-sized barcode files: find ... -name "*_barcode.txt" -size 0. The results is processed and stored in the SkippedTiles annotation as '<lane>:<tile>' on the DemuxedSequences item. If the total number of skipped tiles for a demux is 10 or more a warning message is added to the DemuxWarnings annotation.

The information about skipped tiles is also displayed in the 'Confirm demux' wizard.

Note that this change requires that Picard fork version 4 or higher (​http://dev.thep.lu.se/basehacks/wiki/Picard) is used since otherwise Picard will stop with an error message.