Opened 6 years ago
Closed 6 years ago
#1054 closed enhancement (fixed)
Even more functionality in the Flagged alignment wizard
Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
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Priority: | major | Milestone: | Reggie v4.20 |
Component: | net.sf.basedb.reggie | Keywords: | |
Cc: |
Description (last modified by )
See #1050.
- [Done] Implement possibility to flag and add/modify comments when scheduling re-extractions. Since it takes about a week or more to get the result it is good to be able keep some information about why the re-extraction was made in the first place.
- [Done] Introduce a
DoNotUse
flag that should be set on the top-most item that is considered incorrect. The top-most item is typically a Specimen, Lysate, RNA, PreNormalizedRNA or Library. The flag should then be copied downstreams to all child items. ADoNotUseComment
that goes along with the flag is probably also a good idea.
- [Done] Alignments that are flagged as
DoNotUse
should be removed from theFlagged alignments
list and disabled for future genotype checks. (Update) Disabling is the default, but there should also be an option to keep them available for genotype checks. Remaining items in the list should be checked again and items that no longer get any genotype warning should also be removed.
- A lot of other wizards need to be updated to check the
DoNotUse
flag. For example:- When manually selecting RNA for library preparation a warning should be displayed.
- Demuxing should skip flagged libraries. The rules for generating warnings, etc. need to be updated.
- and more...
Change History (39)
comment:1 by , 6 years ago
Milestone: | Reggie v4.x → Reggie v4.20 |
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comment:2 by , 6 years ago
Description: | modified (diff) |
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Status: | new → assigned |
comment:3 by , 6 years ago
comment:4 by , 6 years ago
(In [4972]) References #1054: Even more functionality in the Flagged alignment wizard
Added two new annotation types: DoNotUse
and DoNotUseComment
.
They should be set on any item (from Specimen all the way down to RawBioassay) to indicate that it should not be used in the future for some reason (as indicated by the comment). The DoNotUse
is a string enumeration with possible values: Specimen
, Lysate
, RNA
, Library
. The value should reflect the top-most item where there is a problem. For example, if an RNA is contaminated, then DoNotUse=RNA
for the RNA and all items downstreams.
comment:5 by , 6 years ago
comment:6 by , 6 years ago
comment:7 by , 6 years ago
(In [4975]) References #1054: Even more functionality in the Flagged alignment wizard
Implemented functionality for marking items as "Ok to use" or "Do not use". The selection can be done on Specimen, Lysate, RNA or Library level and will affect all downstream child items.
The functionality is only available if a filter is active. If the filter is a Qiacube or Libplate filter it is a requirement that an option is selected for all flagged items. If the "Do not use" option is used a comment is required.
comment:8 by , 6 years ago
(In [4976]) References #1054: Even more functionality in the Flagged alignment wizard
Added an indicator for re-processing that is enabled if there is no other alignment for the same specimen. Alignments from the same RNA (if a Qiacube filter is active) or library (if HET filter or libplate filter is active) are not counted as a separate alignment.
When the High HET filter is active there is also an indicator for DoNotUse that is active if there is another alignement without an "error" condition.
comment:9 by , 6 years ago
comment:10 by , 6 years ago
comment:11 by , 6 years ago
comment:12 by , 6 years ago
(In [4980]) References #1054: Even more functionality in the Flagged alignment wizard
Display existing DoNotUse information for alignments. If a re-process option is selected from an item marked as DoNotUse a warning icon is displayed. In the "Resolve" mode alignments marked as DoNotUse can't be modified.
comment:13 by , 6 years ago
(In [4981]) References #1054: Even more functionality in the Flagged alignment wizard
Added an option to keep an alignment that was marked as DoNotUse available for future genotype checks (eg. QC_GENOTYPE_STATUS=Checked
instead of QC_GENOTYPE_STATUS=Disabled
).
For example, if we have a QiaCube shift on positions 8-12, a verified RNA on position 6 but no information about the RNA at position 7 (and no remaining specimen) we can mark it as DoNotUse but keep it enabled for genotype checks in case we get a second sample from the same patient in the future.
Note that there is no possibility yet to change the DoNotUse to OkToUse if the second sample confirms that the original sample was correct.
comment:14 by , 6 years ago
(In [4982]) References #1054: Even more functionality in the Flagged alignment wizard
Added PreNormalizedRNA
as an option for the DoNotUse
annotation. The options is of course only available if the alignment has a pre-normalied RNA item in the parent chain.
A minor complication is present when filtering on a QiaCube. It is possible that alignments from both a pre-normalized and a regular RNA exists and that there is a mixup that only affects the pre-normalized RNA. But the "Resolve" options are grouped by QiaCube positions so there is only one set of options for the two alignments. If the PreNormalizedRNA
option is selected, only the pre-normalized RNA is marked as DoNotUse
and we rely on the auto-unflag option to fix the regular RNA as if the Ok
checkbox had been selected.
comment:15 by , 6 years ago
Description: | modified (diff) |
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comment:16 by , 6 years ago
comment:17 by , 6 years ago
comment:18 by , 6 years ago
(In [4985]) References #1054: Even more functionality in the Flagged alignment wizard
The "Start demux and merge" wizard now checks for libraries marked with DoNotUse. It will display information about them and provide an option to either exclude or include them in the demux. The default is to exclude such libraries.
The actual demux process will still demux all data, but it will collect the data to a virtual library "IGNORED". The main reason for doing this is to avoid that the checks that are made efter the demux to generate warnings for high levels of unmapped reads.
comment:19 by , 6 years ago
comment:20 by , 6 years ago
comment:21 by , 6 years ago
comment:22 by , 6 years ago
comment:23 by , 6 years ago
(In [4993]) References #1054: Even more functionality in the Flagged alignment wizard
The YellowLabel tracking and reporting wizard has been updated to display a warning for items marked with DoNotUse and requires verification if publishing any of those items.
comment:24 by , 6 years ago
comment:25 by , 6 years ago
comment:26 by , 6 years ago
comment:27 by , 6 years ago
comment:28 by , 6 years ago
(In [5001]) References #1054: Even more functionality in the Flagged alignment wizard
Added functionality for keeping track of changes that are made in the forms. Changed elements are highlighted.
A warning message is displayed if there are changes that would be lost due to changing filter settings or navigating to a different page.
comment:29 by , 6 years ago
comment:30 by , 6 years ago
comment:31 by , 6 years ago
comment:32 by , 6 years ago
comment:33 by , 6 years ago
comment:34 by , 6 years ago
(In [5017]) References #1054: Even more functionality in the Flagged alignment wizard
It is now possible to register partial libplates or QiaCubes as resolved. The reason is that there may be more than one mistake that is present on a single batch.
For example, we found a QiaCube run with a single "High HET" item and a swap betweeen 2 other items. The "High HET" is probably a contaminated library and the RNA was already scheduled for re-processing. It should not be solved until the new data is available, but we wanted to solve the swap immediately (marking the two RNA items as DoNotUse).
The possibility to bypass the strict registration rules becomes enabled after trying (and failing) to register an incomplete form. Note that it is only the DoNotUse/OkToUse options that can be bypassed. Comments are still required for all items marked with DoNotUse.
comment:35 by , 6 years ago
comment:36 by , 6 years ago
(In [5024]) References #1054: Even more functionality in the Flagged alignment wizard
It is now possible to repeat a DoNotUse registration. The example use case is as before (see [5017]) that a High HET library is found flagged as DoNotUse. At a later date a swap is discovered that also involves the contaminated library. Before this change it was not possible to re-register a DoNotUse for the RNA since it was disabled due to the library already being flaggd.
This change makes it possible to re-register a DoNotUse flag for all items. Existing flags are not overwritten but it is possible to update the comment by making a second registration. For example, registering a DoNotUse on the RNA will not update anything on items marked with DoNotUse=Library. Repeating the registration one more time with DoNotUse=Library will update the comment on those items.
comment:37 by , 6 years ago
comment:38 by , 6 years ago
comment:39 by , 6 years ago
Resolution: | → fixed |
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Status: | assigned → closed |
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