Y25-202 - scRNA Library Prep Chromium BCR and TCR pipeline config #2299

BenTopping · 2025-04-02T12:29:35Z

Changes proposed in this pull request

Adds scRNA Core Chromium GEM-X 5p BCR and scRNA Core Chromium GEM-X 5p BCR MX pipelines
- Adds pipeline purposes and bed verifications.
Adds scRNA Core Chromium GEM-X 5p TCR and scRNA Core Chromium GEM-X 5p TCR MX pipelines
- Adds pipeline purposes and bed verifications.
Adds custom workflows for BCR and TCR pipelines.

Instructions for Reviewers

Sequencescape PR: sanger/sequencescape#4814
Integration suite PR: https://gitlab.internal.sanger.ac.uk/psd/integration-suite/-/merge_requests/236

…d verifications

codecov · 2025-04-02T12:39:13Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 81.40%. Comparing base (86dcc97) to head (59638f8).
Report is 102 commits behind head on develop.

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@@             Coverage Diff             @@
##           develop    #2299      +/-   ##
===========================================
+ Coverage    81.04%   81.40%   +0.35%     
===========================================
  Files          476      479       +3     
  Lines        18224    18721     +497     
  Branches       269      283      +14     
===========================================
+ Hits         14770    15240     +470     
- Misses        3452     3479      +27     
  Partials         2        2

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…d verifications

…esenter - Changes LRC GEM-X 5p TCR/BCR Dil 2 plate creator to use ConcentrationBinnedPlatePresenter - Updates partial_stamped_plate to accept 'started' request_state for well filter - Updates WellFilterAllowingPartials filter_requests method to check requests exist, not that the parent plate contains requests

BenTopping · 2025-04-03T14:06:51Z

app/models/labware_creators/well_filter_allowing_partials.rb

@@ -15,7 +15,7 @@ def filter_by_state(requests)
  end

  def filter_requests(requests, well)
-    return nil if well.requests_as_source.empty?


This has been looked at before by @andrewsparkes: e4d9e2f. I don't think the existing behaviour is correct because this checks that the parent well contains the request (source of request is parent well). This means this can only be valid if the parent plate is the first plate in the pipeline (submitted on) and I don't think that is correct? I think it just happens that the other pipelines that use this meet that condition.

Interesting, so it will only work if used in the labware creator configured on the second plate in a pipeline (so that the parent plate is the first plate)? e.g. LBC TCR Dil 1 and LRC GEM-X 5p GE Dil.

This line has been flip flopping back and forth - well.requests_as_source.empty? --> requests.empty? --> well.requests_as_source.empty? and here, back again!

It does seem odd to pass in a list of requests, and then re-requery the requests using well.requests_as_source.

Looks like it's called a bit further down the same file:
filter_requests(well.active_requests&.uniq, well)

Need to think/discuss more

Yeah we can discuss.
The labware creator was built for a specific plate at a branch point on the cherrypick plate in a specific pipeline, and works for that. It's not been designed to be generic.
I cannot remember why I had to change that line to get it to work though!
active_requests seems to use requests_as_source about 3 or 4 levels of method calls in. it's horribly complicated though.

for chromium they would create the cherrypick, then do partial submissions on the wells in the cherrypick depending on which of 3 library prep types they wanted to do, hence partials. plus the same well could be submitted for more than one library prep. plus they might come back and repeat.
the well filter is having to filter on request type, library type and state to identify the right wells.

the requests were not in the the aliquots on the cherrypick plate, because as you spotted that is the submission plate, they are in requests_as_source only.

Yeah Katy and I discussed this yesterday and thought it best to create a new labware creator instead of modifying this because at the step we are interested in we aren't using partials so it doesnt make sense to use a partial stamp creator.

app/models/labware_creators/partial_stamped_plate.rb

…c_gem_x_5p_bcr_enrich2_2xspri_to_lrc_gem_x_5p_bcr_dil_2 and hamilton_lrc_gem_x_5p_tcr_enrich2_2xspri_to_lrc_gem_x_5p_tcr_dil_2

…ports

…low names

KatyTaylor

Still need to think about that requests one

config/pipelines/high_throughput_scrna_core_library_prep_chromium_bcr.yml

config/purposes/scrna_core_library_prep_chromium_bcr.yml

config/robots.rb

config/exports/exports.yml

app/models/labware_creators/partial_stamped_plate.rb

KatyTaylor · 2025-04-10T12:42:51Z

app/models/labware_creators/well_filter_allowing_partials.rb

@@ -15,7 +15,7 @@ def filter_by_state(requests)
  end

  def filter_requests(requests, well)
-    return nil if well.requests_as_source.empty?


Interesting, so it will only work if used in the labware creator configured on the second plate in a pipeline (so that the parent plate is the first plate)? e.g. LBC TCR Dil 1 and LRC GEM-X 5p GE Dil.

This line has been flip flopping back and forth - well.requests_as_source.empty? --> requests.empty? --> well.requests_as_source.empty? and here, back again!

It does seem odd to pass in a list of requests, and then re-requery the requests using well.requests_as_source.

Looks like it's called a bit further down the same file:
filter_requests(well.active_requests&.uniq, well)

Need to think/discuss more

…d comments

… handle mid-pipeline concentration binning labware

andrewsparkes · 2025-04-16T10:05:53Z

app/models/labware_creators/concentration_binned_plate_stamp.rb

+  # |E1| conc=33.7  x10=337 (bin 2)  |  |  |  |
+  # +--+--+--~                       +--+--+--~
+  # |G1| conc=25.9  x10=259 (bin 2)  |  |  |  |
+  class ConcentrationBinnedPlateStamp < StampedPlate


I don't like the naming here.
'Binning' means rearranging the samples on transfer into the child plate into new well locations depending on some parameter (by concentration in the original).
'Stamp' means source well = destination well, i.e. A1 to A1, B1 to B1 etc. They are not compatible terms.

Ah ok I wasn't aware thats what binning meant. The only difference in this labware creator is that it inherits from StampedPlate instead of PartialStampedPlate.

andrewsparkes

Can we discuss this story? You can't have a binned stamp, so confused what you are trying to do.
Does the original not work for you? it just looks for wells with the right request type (partial submissions for the original pipeline). But if all the wells have the right request won't it just take them all? Assuming that's what you are after.

BenTopping · 2025-04-16T11:12:34Z

Can we discuss this story? You can't have a binned stamp, so confused what you are trying to do. Does the original not work for you? it just looks for wells with the right request type (partial submissions for the original pipeline). But if all the wells have the right request won't it just take them all? Assuming that's what you are after.

Yes sure. The only difference in this new labware creator compared to the existing one (ConcentrationBinnedPlate) is that it inherits from StampedPlate instead of PartialStampedPlate. This is because partial stamped plate uses a well filter that checks the parent plate is a submitted plate (start of the pipeline / has requests_as_source present). Which this pipeline does not match because we are doing this concentration binning half way down the pipeline. So in essence its the same but we are just changing the wellfilter logic to suit via StampedPlate instead.

…ous config from scrna core library prep

feat(scrna): adds library prep chromium bcr purposes, pipeline and be…

af7f561

…d verifications

BenTopping added 2 commits April 2, 2025 14:30

feat(scrna): adds library prep chromium tcr purposes, pipeline and be…

5713418

…d verifications

BenTopping commented Apr 3, 2025

View reviewed changes

app/models/labware_creators/partial_stamped_plate.rb Outdated Show resolved Hide resolved

BenTopping added 4 commits April 3, 2025 15:12

test(scrna): adds fixed volume diultions export tests for hamilton_lr…

bae0a28

…c_gem_x_5p_bcr_enrich2_2xspri_to_lrc_gem_x_5p_bcr_dil_2 and hamilton_lrc_gem_x_5p_tcr_enrich2_2xspri_to_lrc_gem_x_5p_tcr_dil_2

feat(scrna): adds individual exports to BCR and TCR pipelines

d81fb78

feat(scrna): updates workflow names for bcr/tcr enrich1 to enrich2 ex…

f861452

…ports

feat(scrna): finalises tcr/bcr dil 2 dilutions, updates bcr/tcr workf…

184058d

…low names

BenTopping requested a review from KatyTaylor April 8, 2025 09:48

BenTopping linked an issue Apr 8, 2025 that may be closed by this pull request

BCR and TCR pipeline file downloads (007c) #2280

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BenTopping marked this pull request as ready for review April 8, 2025 09:49

KatyTaylor reviewed Apr 10, 2025

View reviewed changes

BenTopping added 2 commits April 10, 2025 15:47

feat(scrna): updates core library prep bcr and tcr pipeline groups an…

fd0259b

…d comments

feat(scrna): Adds concentration binned plate stamp labware creator to…

859d05b

… handle mid-pipeline concentration binning labware

andrewsparkes reviewed Apr 16, 2025

View reviewed changes

feat(scrna): renames concentration_binned_plate_stamp, removes errone…

59638f8

…ous config from scrna core library prep

BenTopping requested review from KatyTaylor and andrewsparkes April 17, 2025 09:53

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Y25-202 - scRNA Library Prep Chromium BCR and TCR pipeline config #2299

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