Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#825 closed enhancement (fixed)

Optimize library preparation and sequencing wizards for NextSeq

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: blocker Milestone: Reggie v4.0
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

Several wizards in the library preparation and sequencing sections was developed when the HiSeq was the primary sequencer. Now that the HiSeq has been retired and replaced with a NextSeq it usually means that the default options has to be changed before the information can be registered. This is a bit irritating.

Another change is that there is no longer any need for separate registration of clustering and sequencing started. It should be possible to merge those two wizards into one. At the same time the lab protocol may have to be redesigned.

It may also be desirable to move the registration of the RunParameters.xml to the sequencing ended wizard (see #821).

Change History (14)

comment:1 Changed 4 years ago by Nicklas Nordborg

Priority: criticalblocker
Status: newassigned

comment:2 Changed 4 years ago by Nicklas Nordborg

(In [3622]) References #825: Optimize library preparation and sequencing wizards for NextSeq?

Changes to the "Create new mRNA plate":

  • Prelimiary pool layout is set to 1x16offset or NP1x16
  • Amaount of RNA is changed to 0.5 and 1.0
  • Warning level for remaining quantity set to 1.0
  • Removed the "Load from file" feature

comment:3 Changed 4 years ago by Nicklas Nordborg

(In [3623]) References #825: Optimize library preparation and sequencing wizards for NextSeq?

Changes to the "Create flow cells" wizard:

  • Removed "HiSeq?" from the list of presets
  • Removed default values for HiSeq? sequencing cycles
  • Removed check for pool molarity that was only used for HiSeq?
  • Removed automatic flow cell layout used for 4 pools on 2 flow cells with 8 lanes (eg. HiSeq?).

comment:4 Changed 4 years ago by Nicklas Nordborg

(In [3625]) References #825: Optimize library preparation and sequencing wizards for NextSeq?

Changes to the "Lab protocol for clustering and sequencing" wizard:

  • Removed "clustering" from the wizard
  • Merged the clustering and sequencing sections into a single section. "Date", "Operator" and "Cluster gen." fields removed from the clustering section. "First base report" and "Turn around date+time" removed from the sequencing section.
  • Sequencer position "B" replaced with a blank option (for custom) flow cell types.

comment:5 Changed 4 years ago by Nicklas Nordborg

(In [3629]) References #825: Optimize library preparation and sequencing wizards for NextSeq?

Started to change the "Register clustering" wizard into a "Reigster sequencing started" wizard.

  • Only a single flow cell can be registered at a time
  • Changed clustering-related fields into sequencing-related
  • Added "Sequencer position" field

There are more things to do that will have to wait until the "Sequencing ended" wizard has been updated:

  • The wizard should be moved to the "sequencing_started.jsp" file
  • Move code between FlowCellServlet and SequencingRunServlet.

comment:6 Changed 4 years ago by Nicklas Nordborg

(In [3632]) References #825: Optimize library preparation and sequencing wizards for NextSeq?

Started to change the "Register sequencing ended" wizard.

  • The RunParameters.xml is now needed for this step
  • A lot of information is verified against what has already been registered: Flow cell barcode, sequencing cycles, start date, sequencer, position. Mismatches result in a warning icon, but we trust the RunParameters.xml and update the existing information. The only exception is that the flow cell barcode is only allowed to mismatch in character case. A "bigger" mismatch is an error (wrong file selected?) and the registration wizard is stopped.

comment:7 Changed 4 years ago by Nicklas Nordborg

(In [3633]) References #825: Optimize library preparation and sequencing wizards for NextSeq?

Moved sequencing started wizard into 'sequencing_started.jsp' file and removed the old file. Removed code that is no longer used by any of the wizards.

comment:8 Changed 4 years ago by Nicklas Nordborg

(In [3634]) References #825: Optimize library preparation and sequencing wizards for NextSeq?

Remove debug output.

comment:9 Changed 4 years ago by Nicklas Nordborg

(In [3635]) References #825: Optimize library preparation and sequencing wizards for NextSeq?

Updated the "Confirm sequencing completed" wizard.

comment:10 Changed 4 years ago by Nicklas Nordborg

(In [3636]) References #825: Optimize library preparation and sequencing wizards for NextSeq?

If the RunCompletionStatus.xml file exists, use the last modified time of it to set the value for "End date" on the sequencing run.

comment:11 Changed 4 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

comment:12 Changed 4 years ago by Nicklas Nordborg

(In [3663]) References #825: Optimize library preparation and sequencing wizards for NextSeq?

Removed FlowCellSampleSheetExporter. Not really a NextSeq vs. HiSeq change but this exporter has not been used since we started with Picard for demuxing (see [2429]).

comment:13 Changed 4 years ago by Nicklas Nordborg

(In [3664]) References #825: Optimize library preparation and sequencing wizards for NextSeq?

And the configuration for the flow cell exporter should also be removed...

comment:14 Changed 4 years ago by Nicklas Nordborg

(In [3665]) References #825: Optimize library preparation and sequencing wizards for NextSeq?

Remove support for re-mapping 96-well plate to 384-well plates when running Caliper in the library preparation.

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