Opened 6 years ago

Closed 5 years ago

Last modified 5 years ago

#562 closed enhancement (fixed)

Re-design clustering and sequencing startup wizards

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

Description

While working on the secondary analysis wizards (#545 and #546) it became clear that the existing wizards for clustering and sequencing startup need to be modified.

The main issue is that flow cells are not sequenced in pairs. Even if two flow cells are started at the same time, it is considered as two separate sequencing runs (which could have started several days apart). This means that the information (such as start date, run number, etc) can be different and the flow cells can't be grouped together in a single SequencingRun item in BASE.

Another issue is that a flow cell may be re-sequenced. If the 'first base report' is not good there is sometimes a possibility to start a second SequencingRun for the flow cell. The first try should then be registered as failed. In this case the clustering is not so this means that the 'Register clustering and sequencing startup' wizard need to be split in one wizard for the clustering and one wizard for the sequencing start up (which can be run multiple times for the same flow cell, but the 'Register sequencing ended' should set a flag first).

The new 'Register sequencing startup' wizard should be based on information in the runParameters.xml file which contain most of the information that is today entered manually in the existing wizard (eg. flow cell barcode, position, start date, etc).

A result of these changes is that the data that is currently registered is not what we want. A manual procedure is requried to be able to use the new wizards with the existing data and then remove old items that are no longer needed.

Change History (12)

comment:1 Changed 6 years ago by Nicklas Nordborg

Status: newassigned

comment:2 Changed 6 years ago by Nicklas Nordborg

(In [2201]) References #562: Re-design clustering and sequencing startup wizards

New version of the lab protocol. Both the clustering and sequencing sections are now separate for both flow cells. Added fields to the sequencing section for recording first base report, turnaround and end date+time.

comment:3 Changed 6 years ago by Nicklas Nordborg

(In [2202]) References #562: Re-design clustering and sequencing startup wizards

Started to split the "Register clustering and sequencing startup" wizard. The existing registration has been modified to only register clustering information. It has support for registering 1 or 2 flow cells at the same time, but if not the date, operator is the same each flow cell must be separately registered.

comment:4 Changed 6 years ago by Nicklas Nordborg

(In [2222]) References #562: Re-design clustering and sequencing startup wizards

Added check for existing flow cell with same ID in the clustering registration wizard.

comment:5 Changed 6 years ago by Nicklas Nordborg

(In [2224]) References #562: Re-design clustering and sequencing startup wizards

First version of a new 'sequencing startup' wizard. The wizard get most of the required information from the 'runParameters.xml' file that is created by the HiSeq?. The intention is that the registration should be done immediately after the sequencing has started, but it should work to register already finished sequencing runs as well. There is a check so that the same sequencing run is not registered twice (defined by output folder for data files).

A SequencingRun item now always linked to a single FlowCell, but due to restarts a FlowCell may have more than one SequencingRun. If a flow cell is restarted and this results in a new data file folder is created, the wizard should (must!) be used twice.

This update also shifts around some annotations:

  • HiSeqPosition: Moved from FlowCell to SequencingRun.
  • SequencingCycles: Also used on SequencingRun (parsed from 'runParameters.xml'). The value on FlowCell is manually entered in the design phase.
  • SequencingRunNumber: Parsed from 'runParameters.xml' and stored with SequencingRun.
  • DataFilesFolder: Parsed from 'runParameters.xml' and stored with SequencingRun.

comment:6 Changed 6 years ago by Nicklas Nordborg

(In [2227]) References #562: Re-design clustering and sequencing startup wizards

Make sure that the information displayed is from the currently selected runParameters.xml file if the user switches to another file.

comment:7 Changed 6 years ago by Nicklas Nordborg

(In [2231]) References #562: Re-design clustering and sequencing startup wizards

Some minor changes to the layout.

comment:8 Changed 6 years ago by Nicklas Nordborg

(In [2237]) References #562: Re-design clustering and sequencing startup wizards

Load and display information about pools and library plate in the sequencing startup wizard to make it easier to verify that the correct runparameters.xml file has been selected.

comment:9 Changed 6 years ago by Nicklas Nordborg

(In [2239]) References #562: Re-design clustering and sequencing startup wizards

Display a warning icon if the planned SequencingCycles is different from the information in the runParameters.xml file. Registration will overwrite the planned values with the actual values.

comment:10 Changed 6 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:11 Changed 5 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

comment:12 Changed 5 years ago by Nicklas Nordborg

(In [2311]) References #562: Re-design clustering and sequencing startup wizards

Flow cell ID may not be saved in same case as in the RunParameters.xml file. Detect this, use case-insensitive search on PostgreSQL and update the value in the database to match the one in the file.

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