From c677ec1172000b642ba1b6330ac7be47e1e88210 Mon Sep 17 00:00:00 2001 From: Shiv <44001656+SHIV5T3R@users.noreply.github.com> Date: Wed, 28 Aug 2024 11:09:35 +0100 Subject: [PATCH 1/7] Added pipeline config for LCM Triomics EMSeq steps --- .../pipelines/high_throughput_lcm_triomics.wip.yml | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 config/pipelines/high_throughput_lcm_triomics.wip.yml diff --git a/config/pipelines/high_throughput_lcm_triomics.wip.yml b/config/pipelines/high_throughput_lcm_triomics.wip.yml new file mode 100644 index 000000000..2d3e79cc2 --- /dev/null +++ b/config/pipelines/high_throughput_lcm_triomics.wip.yml @@ -0,0 +1,14 @@ +--- +# Pipeline configuration for EMSeq +LCM Triomics DNA Prep: + filters: + request_type_key: limber_lcm_triomics_dna_prep + relationships: + LCMT Lysate: LCMT DNA Adp Lig + +LCM Triomics DNA WGS Library Prep: + filters: + request_type_key: limber_lcm_triomics_dna_wgs_library_prep + library_type: LCM Triomics DNA WGS + relationships: + LCMT DNA Lib PCR: LCM DNA Lib PCR \ No newline at end of file From d5f61458264c08d8991a057b34470ed20018e452 Mon Sep 17 00:00:00 2001 From: Shiv <44001656+SHIV5T3R@users.noreply.github.com> Date: Wed, 28 Aug 2024 11:10:12 +0100 Subject: [PATCH 2/7] Added plate purposes for LCM Triomics EMSeq steps --- config/purposes/lcm_triomics.wip.yml | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 config/purposes/lcm_triomics.wip.yml diff --git a/config/purposes/lcm_triomics.wip.yml b/config/purposes/lcm_triomics.wip.yml new file mode 100644 index 000000000..1c407f7d2 --- /dev/null +++ b/config/purposes/lcm_triomics.wip.yml @@ -0,0 +1,18 @@ +# EMSeq plate purposes +--- +LCMT Lysate: + :asset_type: plate + :stock_plate: true + :cherrypickable_target: false + :input_plate: true + :presenter_class: Presenters::StockPlatePresenter + :creator_class: LabwareCreators::Uncreatable + :size: 96 +LCMT DNA Adp Lig: + :asset_type: plate + :stock_plate: false + :cherrypickable_target: false + :input_plate: false + :state_changer_class: StateChangers::AutomaticPlateStateChanger + :work_completion_request_type: limber_lcm_triomics_dna_prep + :presenter_class: Presenters::PermissivePresenter \ No newline at end of file From 370e7ffc7ab00dfc5faf6bc5cb50d083abb8e713 Mon Sep 17 00:00:00 2001 From: Shiv <44001656+SHIV5T3R@users.noreply.github.com> Date: Wed, 28 Aug 2024 11:17:59 +0100 Subject: [PATCH 3/7] Prettier --- config/pipelines/high_throughput_lcm_triomics.wip.yml | 2 +- config/purposes/lcm_triomics.wip.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/config/pipelines/high_throughput_lcm_triomics.wip.yml b/config/pipelines/high_throughput_lcm_triomics.wip.yml index 2d3e79cc2..ae8269994 100644 --- a/config/pipelines/high_throughput_lcm_triomics.wip.yml +++ b/config/pipelines/high_throughput_lcm_triomics.wip.yml @@ -11,4 +11,4 @@ LCM Triomics DNA WGS Library Prep: request_type_key: limber_lcm_triomics_dna_wgs_library_prep library_type: LCM Triomics DNA WGS relationships: - LCMT DNA Lib PCR: LCM DNA Lib PCR \ No newline at end of file + LCMT DNA Lib PCR: LCM DNA Lib PCR diff --git a/config/purposes/lcm_triomics.wip.yml b/config/purposes/lcm_triomics.wip.yml index 1c407f7d2..8d97a6cba 100644 --- a/config/purposes/lcm_triomics.wip.yml +++ b/config/purposes/lcm_triomics.wip.yml @@ -15,4 +15,4 @@ LCMT DNA Adp Lig: :input_plate: false :state_changer_class: StateChangers::AutomaticPlateStateChanger :work_completion_request_type: limber_lcm_triomics_dna_prep - :presenter_class: Presenters::PermissivePresenter \ No newline at end of file + :presenter_class: Presenters::PermissivePresenter From e7bebd164038143074fed875d971a689e2d8bd4d Mon Sep 17 00:00:00 2001 From: Shiv <44001656+SHIV5T3R@users.noreply.github.com> Date: Wed, 28 Aug 2024 12:33:58 +0100 Subject: [PATCH 4/7] Added remaining config purposes --- config/purposes/lcm_triomics.wip.yml | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/config/purposes/lcm_triomics.wip.yml b/config/purposes/lcm_triomics.wip.yml index 8d97a6cba..97175c623 100644 --- a/config/purposes/lcm_triomics.wip.yml +++ b/config/purposes/lcm_triomics.wip.yml @@ -8,6 +8,25 @@ LCMT Lysate: :presenter_class: Presenters::StockPlatePresenter :creator_class: LabwareCreators::Uncreatable :size: 96 + +LCMT DNA Frag: + :asset_type: plate + :stock_plate: true + :cherrypickable_target: false + :input_plate: true + :presenter_class: Presenters::StockPlatePresenter + :creator_class: LabwareCreators::Uncreatable + :size: 96 + +LCMT DNA End Prep: + :asset_type: plate + :stock_plate: true + :cherrypickable_target: false + :input_plate: true + :presenter_class: Presenters::StockPlatePresenter + :creator_class: LabwareCreators::Uncreatable + :size: 96 + LCMT DNA Adp Lig: :asset_type: plate :stock_plate: false From d59c750101070c83a0f0b1e1230252c42e55371d Mon Sep 17 00:00:00 2001 From: Shiv <44001656+SHIV5T3R@users.noreply.github.com> Date: Wed, 28 Aug 2024 12:44:26 +0100 Subject: [PATCH 5/7] Modified purpose config for LCM Triomics pipeline --- config/purposes/lcm_triomics.wip.yml | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) diff --git a/config/purposes/lcm_triomics.wip.yml b/config/purposes/lcm_triomics.wip.yml index 97175c623..6feb7f999 100644 --- a/config/purposes/lcm_triomics.wip.yml +++ b/config/purposes/lcm_triomics.wip.yml @@ -11,20 +11,18 @@ LCMT Lysate: LCMT DNA Frag: :asset_type: plate - :stock_plate: true + :stock_plate: false :cherrypickable_target: false - :input_plate: true - :presenter_class: Presenters::StockPlatePresenter - :creator_class: LabwareCreators::Uncreatable + :input_plate: false + :presenter_class: Presenters::PermissivePresenter :size: 96 LCMT DNA End Prep: :asset_type: plate - :stock_plate: true + :stock_plate: false :cherrypickable_target: false - :input_plate: true - :presenter_class: Presenters::StockPlatePresenter - :creator_class: LabwareCreators::Uncreatable + :input_plate: false + :presenter_class: Presenters::PermissivePresenter :size: 96 LCMT DNA Adp Lig: @@ -32,6 +30,5 @@ LCMT DNA Adp Lig: :stock_plate: false :cherrypickable_target: false :input_plate: false - :state_changer_class: StateChangers::AutomaticPlateStateChanger - :work_completion_request_type: limber_lcm_triomics_dna_prep :presenter_class: Presenters::PermissivePresenter + :size: 96 From 583ff1024cc3ae6a985789f88547301944eaa85e Mon Sep 17 00:00:00 2001 From: Shiv <44001656+SHIV5T3R@users.noreply.github.com> Date: Wed, 28 Aug 2024 12:50:32 +0100 Subject: [PATCH 6/7] Modified relationships for pipeline config --- .../high_throughput_lcm_triomics.wip.yml | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/config/pipelines/high_throughput_lcm_triomics.wip.yml b/config/pipelines/high_throughput_lcm_triomics.wip.yml index ae8269994..cec7aa21e 100644 --- a/config/pipelines/high_throughput_lcm_triomics.wip.yml +++ b/config/pipelines/high_throughput_lcm_triomics.wip.yml @@ -1,14 +1,9 @@ --- # Pipeline configuration for EMSeq -LCM Triomics DNA Prep: +LCM Triomics: filters: - request_type_key: limber_lcm_triomics_dna_prep + request_type_key: limber_lcm_triomics relationships: - LCMT Lysate: LCMT DNA Adp Lig - -LCM Triomics DNA WGS Library Prep: - filters: - request_type_key: limber_lcm_triomics_dna_wgs_library_prep - library_type: LCM Triomics DNA WGS - relationships: - LCMT DNA Lib PCR: LCM DNA Lib PCR + LCMT Lysate: LCMT DNA Frag + LCMT DNA Frag: LCMT DNA End Prep + LCMT DNA End Prep: LCMT DNA Adp Lig From 1dad93213771997f8e6c9fd2bd0111bc636e6303 Mon Sep 17 00:00:00 2001 From: Shiv <44001656+SHIV5T3R@users.noreply.github.com> Date: Wed, 4 Sep 2024 09:59:52 +0100 Subject: [PATCH 7/7] Changed pipeline name and added pipeline group --- config/pipelines/high_throughput_lcm_triomics.wip.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/config/pipelines/high_throughput_lcm_triomics.wip.yml b/config/pipelines/high_throughput_lcm_triomics.wip.yml index cec7aa21e..9eff21a8d 100644 --- a/config/pipelines/high_throughput_lcm_triomics.wip.yml +++ b/config/pipelines/high_throughput_lcm_triomics.wip.yml @@ -1,9 +1,10 @@ --- # Pipeline configuration for EMSeq -LCM Triomics: +LCM Triomics EMSeq: filters: - request_type_key: limber_lcm_triomics + request_type_key: limber_lcm_triomics_emseq relationships: LCMT Lysate: LCMT DNA Frag LCMT DNA Frag: LCMT DNA End Prep LCMT DNA End Prep: LCMT DNA Adp Lig + pipeline_group: LCM Triomics WGS and EMSeq