Opened 6 years ago

Closed 5 years ago

Last modified 5 years ago

#499 closed task (fixed)

Export sample sheet for flow cell

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v2.13
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

The sample sheet is a tab-separated text file with data about the samples that are put into a flow cell, including information about barcoding. The sample sheet is used by analysis software after the sequencing.

Change History (8)

comment:1 Changed 6 years ago by Nicklas Nordborg

Status: newassigned

comment:2 Changed 6 years ago by Nicklas Nordborg

(In [2021]) References #499: Export sample sheet for flow cell

First implementation of an export plug-in. It is yet a bit uncertain were some information should be coming from. Eg. the ReadString? is now configuration parameter for the plug-in, but it may be better to store this as an annotation on the flow cell (as is done for 'operator' and 'flow cell id'). Some information is still hard-coded in the plug-in (eg. concentration = 12pM).

comment:3 Changed 6 years ago by Nicklas Nordborg

(In [2030]) References #499: Export sample sheet for flow cell

The exporter now uses the ReadString? stored as an annotation to the Flow cell instead of asking for it as a job parameter.

comment:4 Changed 6 years ago by Nicklas Nordborg

(In [2075]) References #499: Export sample sheet for flow cell

Removed hardcoded concentration of "12pM" and made it a job/configuration parameter instead.

comment:5 Changed 6 years ago by Nicklas Nordborg

(In [2076]) References #499: Export sample sheet for flow cell

Better progress reporter for flow cells of size != 8.

comment:6 Changed 6 years ago by Nicklas Nordborg

(In [2088]) References #499: Export sample sheet for flow cell

Added ReadString as a parameter to the sample sheet exporter.

comment:7 Changed 5 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

comment:8 Changed 5 years ago by Nicklas Nordborg

(In [2105]) References #499: Export sample sheet for flow cell

The ReadString parameter is now calculated automatically from the SequencingCycles values. It is assumed that the SequencingCycles consists of 3 values separated by '-'. The first and last values are normal reads and use 'Y'/'N' and the middle value is index read and use 'I' and 'J'. Each value is subtracted by one and used for the 'Y' or 'I' part. Then 'N1' or 'J1' is added.

If it is not possible to calculate the ReadString the default value 'Y54N1I6J1Y53N1' is used.

For this to work, the plug-in configuration can no longer have any parameter for the ReadString since it has higher priority than the default values.

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