#481 closed task (fixed)
Register prepared flow cells
Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
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Priority: | critical | Milestone: | Reggie v2.13 |
Component: | net.sf.basedb.reggie | Keywords: | |
Cc: |
Description (last modified by )
Change History (20)
comment:1 Changed 10 years ago by
Status: | new → assigned |
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comment:2 Changed 10 years ago by
Milestone: | Reggie v2.12 → Reggie v2.13 |
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comment:4 Changed 10 years ago by
Description: | modified (diff) |
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Priority: | major → critical |
comment:5 Changed 10 years ago by
(In [2031]) References #481: Register prepared flow cells
Added fields for "FlowCellID", "ReadString?" and sequence start date/operator when registering flow cells. But so far, only some of the information is saved in the database.
Not sure if we should introduce a DERIVEDBIOASSAY to represent the sequencing already at this point. If so, it would make sense to register the start date and operator on this item instead of on the flow cells.
Failure to cluster a flow cell is also not handled vere well at the moment.
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(In [2057]) References #481: Register prepared flow cells
Added support for registering the HiSeq? used for sequencing. Actual hardware items must be created by the server administrator with the subtype 'Sequencer'. Automatic selection follow the same pattern as for protocols, eg. the last added item which is set as 'project default' is the default choice.
comment:8 Changed 10 years ago by
(In [2059]) References #481: Register prepared flow cells
Re-organized the registration wizard. There are now three steps instead of two. The first step is the same for selecting flow cells. The second step is for clustering information. The third step is for sequence startup information and is skipped if the 'Failed' option is selected.
Comments in the clustering step can now be made per flow cell.
A protocol can now be specified for the sequencing step.
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(In [2077]) References #481: Register prepared flow cells
Implemented support for registering a failed clustering. The pools on the flow cells are flagged with ClusteringFailed
annotation and put into the Flagged PooledLibrary
biomaterial list. The "Create flow cells" wizard has been modified to ignore flagged pools unless they also have been annotated with AutoProcess=ReProcess
.
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Resolution: | → fixed |
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Status: | assigned → closed |
comment:19 Changed 10 years ago by
comment:20 Changed 10 years ago by
(In [2109]) References #502 and #481.
Added PooledLibraryAliquot
subtype which must be used by the intermediary aliquots connecting flow cells with pooled libraries. This is required so that we can maintain an unbroken link of related subtypes. The previous version linked FlowCell
directly to PooledLibrary
which was incorrect.
The registration wizard now also sets the creation date for the aliquots to the ClusterDate
.
Existing aliquot items should be updated manually or by a batch importer to set subtype=PooledLibraryAliquot
and creation date=ClusterDate
(taken from the flow cell the aliquot is used on).
(In [2020]) References #481: Register prepared flow cells
Preliminary wizards for flow cell creation and registration.
NOTE! Part of this work belong to #502 but that ticket wasn't created until later.