Optimize library preparation and sequencing wizards for NextSeq

[Nicklas Nordborg]

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).

[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

[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).

[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.

[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.

[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.

[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.

[Nicklas Nordborg]

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

Remove debug output.

[Nicklas Nordborg]

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

Updated the "Confirm sequencing completed" wizard.

• Removed "FirstBaseReportFailed" option

[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.

[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]).

[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...

[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.