From 7946080e764f9ca783528447371c5bbd0933041d Mon Sep 17 00:00:00 2001 From: Wendy Yang Date: Mon, 9 Sep 2024 16:38:35 +0100 Subject: [PATCH 1/4] add stock plate as limber plate --- config/pipelines/bespoke_pcr.yml | 1 + config/purposes/bespoke.yml | 5 +++++ 2 files changed, 6 insertions(+) diff --git a/config/pipelines/bespoke_pcr.yml b/config/pipelines/bespoke_pcr.yml index 2911e36de..aee28c6c1 100644 --- a/config/pipelines/bespoke_pcr.yml +++ b/config/pipelines/bespoke_pcr.yml @@ -34,6 +34,7 @@ Bespoke PCR: - TruSeq mRNA (RNA Seq) library_pass: LBB Lib PCR-XP relationships: + Stock Plate: LBB Ligation LBB Cherrypick: LBB Ligation LBC Cherrypick: LBB Ligation LBB Ligation: LBB Lib PCR-XP diff --git a/config/purposes/bespoke.yml b/config/purposes/bespoke.yml index 5a4411904..fc21a0aeb 100644 --- a/config/purposes/bespoke.yml +++ b/config/purposes/bespoke.yml @@ -43,3 +43,8 @@ LBB Enriched TCR: LBB Enriched TCR HT: :asset_type: plate :creator_class: LabwareCreators::PartialStampedPlateWithoutDilution +Stock Plate: + :asset_type: plate + :stock_plate: true + :input_plate: true + :presenter_class: Presenters::StockPlatePresenter From dd2bd0ddaeaba7ae069a14a860c4223d1ad5ddff Mon Sep 17 00:00:00 2001 From: Wendy Yang Date: Wed, 11 Sep 2024 11:59:48 +0100 Subject: [PATCH 2/4] separate stock plate just for 10x - CITEseq and Emseq pipelines --- config/pipelines/bespoke_pcr.yml | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/config/pipelines/bespoke_pcr.yml b/config/pipelines/bespoke_pcr.yml index aee28c6c1..4530fc923 100644 --- a/config/pipelines/bespoke_pcr.yml +++ b/config/pipelines/bespoke_pcr.yml @@ -34,10 +34,22 @@ Bespoke PCR: - TruSeq mRNA (RNA Seq) library_pass: LBB Lib PCR-XP relationships: - Stock Plate: LBB Ligation LBB Cherrypick: LBB Ligation LBC Cherrypick: LBB Ligation LBB Ligation: LBB Lib PCR-XP + +Bespoke PCR Stock plate: + pipeline_group: Bespoke PCR + filters: + request_type_key: limber_pcr_bespoke + library_type: + - Chromium single cell surface protein + - emSEQ + library_pass: LBB Lib PCR-XP + relationships: + Stock Plate: LBB Ligation + LBB Ligation: LBB Lib PCR-XP + Bespoke PCR BCR: filters: request_type_key: limber_pcr_bespoke From 56c7ee186f2deab9f043bd083b3c0c2106c1ffb6 Mon Sep 17 00:00:00 2001 From: Wendy Yang Date: Wed, 11 Sep 2024 19:49:01 +0100 Subject: [PATCH 3/4] extend stock plate as input plate to other pipelines --- config/pipelines/bespoke_pcr.yml | 17 +++++------------ 1 file changed, 5 insertions(+), 12 deletions(-) diff --git a/config/pipelines/bespoke_pcr.yml b/config/pipelines/bespoke_pcr.yml index 4530fc923..77dc621ef 100644 --- a/config/pipelines/bespoke_pcr.yml +++ b/config/pipelines/bespoke_pcr.yml @@ -34,22 +34,11 @@ Bespoke PCR: - TruSeq mRNA (RNA Seq) library_pass: LBB Lib PCR-XP relationships: + Stock Plate: LBB Ligation LBB Cherrypick: LBB Ligation LBC Cherrypick: LBB Ligation LBB Ligation: LBB Lib PCR-XP -Bespoke PCR Stock plate: - pipeline_group: Bespoke PCR - filters: - request_type_key: limber_pcr_bespoke - library_type: - - Chromium single cell surface protein - - emSEQ - library_pass: LBB Lib PCR-XP - relationships: - Stock Plate: LBB Ligation - LBB Ligation: LBB Lib PCR-XP - Bespoke PCR BCR: filters: request_type_key: limber_pcr_bespoke @@ -57,6 +46,7 @@ Bespoke PCR BCR: - Manual Chromium single cell BCR library_pass: LBB Lib PCR-XP relationships: + Stock Plate: LBB Enriched BCR LBB Cherrypick: LBB Enriched BCR LBC Cherrypick: LBB Enriched BCR LBB Enriched BCR: LBB Ligation @@ -68,6 +58,7 @@ Bespoke PCR BCR HT: - Manual Chromium single cell BCR HT library_pass: LBB Lib PCR-XP relationships: + Stock Plate: LBB Enriched BCR HT LBB Cherrypick: LBB Enriched BCR HT LBC Cherrypick: LBB Enriched BCR HT LBB Enriched BCR HT: LBB Ligation @@ -79,6 +70,7 @@ Bespoke PCR TCR: - Manual Chromium single cell TCR library_pass: LBB Lib PCR-XP relationships: + Stock Plate: LBB Enriched TCR LBB Cherrypick: LBB Enriched TCR LBC Cherrypick: LBB Enriched TCR LBB Enriched TCR: LBB Ligation @@ -90,6 +82,7 @@ Bespoke PCR TCR HT: - Manual Chromium single cell TCR HT library_pass: LBB Lib PCR-XP relationships: + Stock Plate: LBB Enriched TCR HT LBB Cherrypick: LBB Enriched TCR HT LBC Cherrypick: LBB Enriched TCR HT LBB Enriched TCR HT: LBB Ligation From e31e4ad42d2c0600fb1cf3fa9ede55f6c6205ace Mon Sep 17 00:00:00 2001 From: Wendy Yang Date: Wed, 11 Sep 2024 20:02:36 +0100 Subject: [PATCH 4/4] fix formating --- config/pipelines/bespoke_pcr.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/config/pipelines/bespoke_pcr.yml b/config/pipelines/bespoke_pcr.yml index 77dc621ef..ba17dfe0e 100644 --- a/config/pipelines/bespoke_pcr.yml +++ b/config/pipelines/bespoke_pcr.yml @@ -46,7 +46,7 @@ Bespoke PCR BCR: - Manual Chromium single cell BCR library_pass: LBB Lib PCR-XP relationships: - Stock Plate: LBB Enriched BCR + Stock Plate: LBB Enriched BCR LBB Cherrypick: LBB Enriched BCR LBC Cherrypick: LBB Enriched BCR LBB Enriched BCR: LBB Ligation @@ -58,7 +58,7 @@ Bespoke PCR BCR HT: - Manual Chromium single cell BCR HT library_pass: LBB Lib PCR-XP relationships: - Stock Plate: LBB Enriched BCR HT + Stock Plate: LBB Enriched BCR HT LBB Cherrypick: LBB Enriched BCR HT LBC Cherrypick: LBB Enriched BCR HT LBB Enriched BCR HT: LBB Ligation @@ -70,7 +70,7 @@ Bespoke PCR TCR: - Manual Chromium single cell TCR library_pass: LBB Lib PCR-XP relationships: - Stock Plate: LBB Enriched TCR + Stock Plate: LBB Enriched TCR LBB Cherrypick: LBB Enriched TCR LBC Cherrypick: LBB Enriched TCR LBB Enriched TCR: LBB Ligation @@ -82,7 +82,7 @@ Bespoke PCR TCR HT: - Manual Chromium single cell TCR HT library_pass: LBB Lib PCR-XP relationships: - Stock Plate: LBB Enriched TCR HT + Stock Plate: LBB Enriched TCR HT LBB Cherrypick: LBB Enriched TCR HT LBC Cherrypick: LBB Enriched TCR HT LBB Enriched TCR HT: LBB Ligation