Opened 6 years ago

Closed 6 years ago

Last modified 6 years ago

#631 closed enhancement (fixed)

Add data check to the confirm sequencing ended wizard

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v2.16
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

Picard has a tool called CheckIlluminaDirectory which can be used for a quick check that the expected data files are present and seems reasonable. It would be nice to be able to use this tool from the "Confirm sequencing completed" wizard before deciding if a sequencing run has succeeded or not.

Change History (6)

comment:1 Changed 6 years ago by Nicklas Nordborg

(In [2641]) References #631: Add data check to the confirm sequencing ended wizard

This more or less implements this feature. But it also requires an updated/modified Picard version due to the 'InterOp?' directories in our run archive are different. For example, in most of the older ones the TileMetrics.bin and TileMetricsOut.bin are identical. The latter file is used by Picard in the validation to find information about tiles.

In newer runs, the TileMetricsOut.bin is only 12 bytes and Picard fails saying that there are 0 tiles... The TileMetrics.bin is much larger and more similar in size to the old runs. Don't know the reason for it, but when Picard was told to use the TileMetrics.bin file instead the validation seems to work.

For changes to Picard see: https://github.com/nnordborg/picard/commit/5cdb8b1232052d35bc2d533af9944324966b4aaf

comment:2 Changed 6 years ago by Nicklas Nordborg

(In [2642]) References #631: Add data check to the confirm sequencing ended wizard

Added the check button to the "Start demux and merge" wizard. The check also parses the information from a successful check and tries to verify the number of tiles and cycles.

comment:3 Changed 6 years ago by Nicklas Nordborg

(In [2643]) References #631: Add data check to the confirm sequencing ended wizard

Lane counter was not correctly reset after all checks are completed.

comment:4 Changed 6 years ago by Nicklas Nordborg

(In [2645]) References #631: Add data check to the confirm sequencing ended wizard

Line wrap in error messages makes them easier to display. Re-organized code that performs the checking.

comment:5 Changed 6 years ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed

comment:6 Changed 6 years ago by Nicklas Nordborg

(In [2729]) References #547, #593 and #631. Check that values from the database such as paths and names of items are safe to use in scripts. The check is currently very strict and only allow letters, digits, dot, underscore and hyphen.

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