Opened 7 years ago

Closed 7 years ago

#546 closed task (fixed)

Confirm sequencing as completed

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v2.15
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

Part of #533.

This is the first wizard in the "Secondary analysis wizards" section. It can be used by users with the SecondaryAnalysis role.

The purpose of the wizard is to decide if the sequenced data is ok or not. If ok, continue with demuxing, otherwise flag pools for re-sequencing.

The wizard should show SequencingRun items that has a SequencingEnd date annotation but no SequencingResult annotation.

At this step we should register the following information on the SequencingRun item:

  • SequencingResult: Enumeration (Success, Failed)
  • Comments: Description column
  • Failed lanes: Multi-valued integer annoation???

If it is decided that the sequencing was not successful, flag PooledLibrary items with Flag=SequencingFailed, otherwise continue with the demux and merge wizard.

Change History (8)

comment:1 Changed 7 years ago by Nicklas Nordborg

(In [2226]) References #546: Confirm sequencing as completed

First version of 'Confirm sequencing completed' wizard. It's really simple. After selecting if a sequencing failed or succeeded there is a field for comments and a possibility to mark individual lanes as failed (if the sequencing was otherwise successful).

comment:2 Changed 7 years ago by Nicklas Nordborg

Status: newassigned

comment:3 Changed 7 years ago by Nicklas Nordborg

(In [2228]) References #546: Confirm sequencing as completed

New version of the 'confirm sequencing' wizard. Introduced a new annotation SequencingConfirmed (boolean) to fix the issue with sequencing runs not showing up for confirmation if FirstBaseReportFailed was set in the 'sequencing ended' wizard.

comment:4 Changed 7 years ago by Nicklas Nordborg

(In [2229]) References #546: Confirm sequencing as completed

Display sequencing start date in the selection list and comments to make it easier to select the correct sequencing run.

comment:5 Changed 7 years ago by Nicklas Nordborg

(In [2235]) References #546: Confirm sequencing as completed

Adding an option to let the user decide if a pool should be flagged or not.

comment:6 Changed 7 years ago by Nicklas Nordborg

(In [2236]) References #545 and #546. Load and display information about pools and library plate to make it easier to relate a sequencing run to the correct lab protocols.

comment:7 Changed 7 years ago by Nicklas Nordborg

(In [2241]) References #562, #545 and #546. Only display pool name once if the flow cell only contains one pool.

comment:8 Changed 7 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed
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