Opened 6 years ago

Closed 6 years ago

#594 closed enhancement (fixed)

Changes for NextSeq support

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v2.15.1
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

A new NextSeq machine is arriving soon. There are some changes we must make in the wizards.

Create flow cells

  • Number of lanes is 4 (but may be 1 depending on how the result files are stored); only one pool per flow cell is allowed
  • Option for HiSeq vs. NextSeq so that we know this and can take actions in downstream wizards (if needed)

Lab protocol for clustering and sequencing

  • It should be noted on the protocol if this is a HiSeq or NextSeq run. Otherwise leave it as it is for now.

Register clustering

  • The flow cell selection should indicate if it is a HiSeq or NextSeq run. NextSeq runs must be registered one by one.

Register sequencing started

  • If we need to change this wizard depends on if the runParameters.xml file is compatible with the HiSeq or not.

Change History (5)

comment:1 Changed 6 years ago by Nicklas Nordborg

Status: newassigned

The RunParameters.xml file from the NextSeq is not compatible with the one from HiSeq. But all information we need is present, it is just inside different tags so this should not really be any problem to detect and adjust to.

comment:2 Changed 6 years ago by Nicklas Nordborg

It has also been confirmed that data output is for 4 lanes, even though all lanes must contain the same sample. The 'Create flow cells' wizard should not be allowed to select more than one pool when working with NextSeq and it should not be possible to set any of the lanes to 'empty'.

comment:3 Changed 6 years ago by Nicklas Nordborg

(In [2408]) References #594: Changes for NextSeq? support

  • Added 'Lanes/flow cell: 4' option in the create flow cell wizard
  • Added 'Flow cell type' parameter to create flow cell wizard-->saved as FlowCellType annotation on the flow cell
  • Minor display changes in the lab protocol wizard
  • Minor display changes in the register clustering wizard
  • Load SEQUENCER items instead of CLUSTER_GENERATOR items when registering NextSeq flow cells in the clustering wizard
  • Updated XML parser in sequencing started wizard to also accept XML files from the NextSeq
  • Minor display changes in the register sequencing ended and confirm sequencing ended wizards

comment:4 Changed 6 years ago by Nicklas Nordborg

(In [2409]) References #594: Changes for NextSeq? support

Hide 'B' position when using NextSeq?.

comment:5 Changed 6 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed
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