From 8b27173ffed4a1a90987fa264909cb145c2a86f0 Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Thu, 21 Nov 2024 15:44:58 +0000 Subject: [PATCH 01/23] Adding new request type and submission --- .../020_limber_high_throughput_bge.wip.yml | 16 ++++++++++++++++ .../submission_templates/016_bge.wip.yml | 7 +++++++ 2 files changed, 23 insertions(+) create mode 100644 config/default_records/request_types/020_limber_high_throughput_bge.wip.yml create mode 100644 config/default_records/submission_templates/016_bge.wip.yml diff --git a/config/default_records/request_types/020_limber_high_throughput_bge.wip.yml b/config/default_records/request_types/020_limber_high_throughput_bge.wip.yml new file mode 100644 index 0000000000..b701ea3753 --- /dev/null +++ b/config/default_records/request_types/020_limber_high_throughput_bge.wip.yml @@ -0,0 +1,16 @@ +--- +limber_bge_pcr_free: + asset_type: Well + order: 1 + request_class_name: IlluminaHtp::Requests::StdLibraryRequest + billable: true + product_line_name: Illumina-HTP + name: Limber BGE PCR Free + acceptable_purposes: + - PF Cherrypicked + library_types: + - HiSeqX PCR free + - Chromium single cell CNV + - DAFT-seq + - PCR Free 384 + - BGE \ No newline at end of file diff --git a/config/default_records/submission_templates/016_bge.wip.yml b/config/default_records/submission_templates/016_bge.wip.yml new file mode 100644 index 0000000000..89d2e192b4 --- /dev/null +++ b/config/default_records/submission_templates/016_bge.wip.yml @@ -0,0 +1,7 @@ +Limber-Htp - GBE PCR Free: + name: "Limber-Htp - GBE PCR Free" + submission_class_name: "LinearSubmission" + related_records: + product_line_name: Illumina-HTP + product_catalogue_name: PFHSqX + request_type_keys: ["limber_bge_pcr_free", "limber_multiplexing", "illumina_htp_novaseqx_paired_end_sequencing"] \ No newline at end of file From 49ad22d7ad73288388fdbb22522e44eb638a265a Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Thu, 21 Nov 2024 15:50:39 +0000 Subject: [PATCH 02/23] Adding new request type and submission --- .../020_limber_high_throughput_bge.wip.yml | 15 ++++++++++++++- .../submission_templates/016_bge.wip.yml | 11 +++++++++-- 2 files changed, 23 insertions(+), 3 deletions(-) diff --git a/config/default_records/request_types/020_limber_high_throughput_bge.wip.yml b/config/default_records/request_types/020_limber_high_throughput_bge.wip.yml index b701ea3753..86ba52aa01 100644 --- a/config/default_records/request_types/020_limber_high_throughput_bge.wip.yml +++ b/config/default_records/request_types/020_limber_high_throughput_bge.wip.yml @@ -13,4 +13,17 @@ limber_bge_pcr_free: - Chromium single cell CNV - DAFT-seq - PCR Free 384 - - BGE \ No newline at end of file + - BGE +limber_bge_isc: + asset_type: Well + order: 1 + billable: true + product_line_name: Illumina-HTP + name: Limber BGE ISC + request_class_name: Pulldown::Requests::IscLibraryRequest + acceptable_purposes: + - LB Cherrypick + library_types: + - Agilent Pulldown + - Twist Pulldown + - BGE diff --git a/config/default_records/submission_templates/016_bge.wip.yml b/config/default_records/submission_templates/016_bge.wip.yml index 89d2e192b4..2a5ae3fa16 100644 --- a/config/default_records/submission_templates/016_bge.wip.yml +++ b/config/default_records/submission_templates/016_bge.wip.yml @@ -1,7 +1,14 @@ -Limber-Htp - GBE PCR Free: +Limber-Htp - BGE PCR Free - NovaSeqX paired end sequencing: name: "Limber-Htp - GBE PCR Free" submission_class_name: "LinearSubmission" related_records: product_line_name: Illumina-HTP product_catalogue_name: PFHSqX - request_type_keys: ["limber_bge_pcr_free", "limber_multiplexing", "illumina_htp_novaseqx_paired_end_sequencing"] \ No newline at end of file + request_type_keys: ["limber_bge_pcr_free", "limber_multiplexing", "illumina_htp_novaseqx_paired_end_sequencing"] +Limber-Htp - BGE ISC - NovaSeqX paired end sequencing: + name: "Limber-Htp - ISC - NovaSeqX paired end sequencing" + submission_class_name: "LinearSubmission" + related_records: + product_line_name: Illumina-HTP + product_catalogue_name: ISC + request_type_keys: ["limber_bge_isc", "limber_multiplexing", "illumina_htp_novaseqx_paired_end_sequencing"] From 1cb1ad880d4cf221b4cb0df6309b0bfb5c6526b0 Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Fri, 22 Nov 2024 11:07:47 +0000 Subject: [PATCH 03/23] Adding new request type and submission --- .../020_limber_high_throughput_bge.wip.yml | 19 +++++++++++++------ .../submission_templates/016_bge.wip.yml | 15 +++++++++++---- 2 files changed, 24 insertions(+), 10 deletions(-) diff --git a/config/default_records/request_types/020_limber_high_throughput_bge.wip.yml b/config/default_records/request_types/020_limber_high_throughput_bge.wip.yml index 86ba52aa01..6a2144b516 100644 --- a/config/default_records/request_types/020_limber_high_throughput_bge.wip.yml +++ b/config/default_records/request_types/020_limber_high_throughput_bge.wip.yml @@ -9,10 +9,19 @@ limber_bge_pcr_free: acceptable_purposes: - PF Cherrypicked library_types: - - HiSeqX PCR free - - Chromium single cell CNV - - DAFT-seq - - PCR Free 384 + - BGE +# For moving PCR Free plates to ISC plates +# e.g., BGE Lib XP2 -> BGE LIB PCR +limber_bge_transition: + asset_type: Well + order: 1 + billable: true + product_line_name: Illumina-HTP + name: Limber BGE Transition + request_class_name: IlluminaHtp::Requests::StdLibraryRequest + acceptable_purposes: + - LB Cherrypick + library_types: - BGE limber_bge_isc: asset_type: Well @@ -24,6 +33,4 @@ limber_bge_isc: acceptable_purposes: - LB Cherrypick library_types: - - Agilent Pulldown - - Twist Pulldown - BGE diff --git a/config/default_records/submission_templates/016_bge.wip.yml b/config/default_records/submission_templates/016_bge.wip.yml index 2a5ae3fa16..4a9ba65b40 100644 --- a/config/default_records/submission_templates/016_bge.wip.yml +++ b/config/default_records/submission_templates/016_bge.wip.yml @@ -1,14 +1,21 @@ -Limber-Htp - BGE PCR Free - NovaSeqX paired end sequencing: +Limber-Htp - BGE PCR Free: name: "Limber-Htp - GBE PCR Free" submission_class_name: "LinearSubmission" related_records: product_line_name: Illumina-HTP product_catalogue_name: PFHSqX request_type_keys: ["limber_bge_pcr_free", "limber_multiplexing", "illumina_htp_novaseqx_paired_end_sequencing"] -Limber-Htp - BGE ISC - NovaSeqX paired end sequencing: - name: "Limber-Htp - ISC - NovaSeqX paired end sequencing" - submission_class_name: "LinearSubmission" +Limber-Htp - BGE ISC: + name: "Limber-Htp - BGE ISC " + submission_class_name: "AutomatedOrder" related_records: product_line_name: Illumina-HTP product_catalogue_name: ISC request_type_keys: ["limber_bge_isc", "limber_multiplexing", "illumina_htp_novaseqx_paired_end_sequencing"] +Limber-Htp - BGE Transition: + name: "Limber-Htp - BGE Transition " + submission_class_name: "AutomatedOrder" + related_records: + product_line_name: Illumina-HTP + product_catalogue_name: ISC # Different product catalogue? + request_type_keys: ["limber_bge_transition"] # Other request types? \ No newline at end of file From 43c47fe672f538887429f8560aeeec0f69667f7e Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Fri, 22 Nov 2024 11:09:14 +0000 Subject: [PATCH 04/23] Making prettier happy --- config/default_records/submission_templates/016_bge.wip.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/default_records/submission_templates/016_bge.wip.yml b/config/default_records/submission_templates/016_bge.wip.yml index 4a9ba65b40..37fd00f05c 100644 --- a/config/default_records/submission_templates/016_bge.wip.yml +++ b/config/default_records/submission_templates/016_bge.wip.yml @@ -18,4 +18,4 @@ Limber-Htp - BGE Transition: related_records: product_line_name: Illumina-HTP product_catalogue_name: ISC # Different product catalogue? - request_type_keys: ["limber_bge_transition"] # Other request types? \ No newline at end of file + request_type_keys: ["limber_bge_transition"] # Other request types? From 14fcbb2fe212db65830fa47794e0bf1bd58f1ab9 Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Fri, 22 Nov 2024 11:32:54 +0000 Subject: [PATCH 05/23] Adding new request type and submission --- .../request_types/020_limber_high_throughput_bge.wip.yml | 1 + config/default_records/submission_templates/016_bge.wip.yml | 3 ++- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/config/default_records/request_types/020_limber_high_throughput_bge.wip.yml b/config/default_records/request_types/020_limber_high_throughput_bge.wip.yml index 6a2144b516..a955171896 100644 --- a/config/default_records/request_types/020_limber_high_throughput_bge.wip.yml +++ b/config/default_records/request_types/020_limber_high_throughput_bge.wip.yml @@ -1,4 +1,5 @@ --- +# Y24-366 limber_bge_pcr_free: asset_type: Well order: 1 diff --git a/config/default_records/submission_templates/016_bge.wip.yml b/config/default_records/submission_templates/016_bge.wip.yml index 37fd00f05c..d3af2603ea 100644 --- a/config/default_records/submission_templates/016_bge.wip.yml +++ b/config/default_records/submission_templates/016_bge.wip.yml @@ -1,3 +1,4 @@ +# Y24-366 Limber-Htp - BGE PCR Free: name: "Limber-Htp - GBE PCR Free" submission_class_name: "LinearSubmission" @@ -11,7 +12,7 @@ Limber-Htp - BGE ISC: related_records: product_line_name: Illumina-HTP product_catalogue_name: ISC - request_type_keys: ["limber_bge_isc", "limber_multiplexing", "illumina_htp_novaseqx_paired_end_sequencing"] + request_type_keys: ["limber_bge_isc", "limber_multiplexing", "illumina_htp_novaseqx_paired_end_sequencing"] # Other request types? Limber-Htp - BGE Transition: name: "Limber-Htp - BGE Transition " submission_class_name: "AutomatedOrder" From ff622b94ef339077363de8853c694f990a833ac7 Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Mon, 25 Nov 2024 09:58:46 +0000 Subject: [PATCH 06/23] Update submission templates to remove deprecated request types and clarify naming --- config/default_records/submission_templates/016_bge.wip.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/config/default_records/submission_templates/016_bge.wip.yml b/config/default_records/submission_templates/016_bge.wip.yml index d3af2603ea..ffeb2eb7dc 100644 --- a/config/default_records/submission_templates/016_bge.wip.yml +++ b/config/default_records/submission_templates/016_bge.wip.yml @@ -5,7 +5,7 @@ Limber-Htp - BGE PCR Free: related_records: product_line_name: Illumina-HTP product_catalogue_name: PFHSqX - request_type_keys: ["limber_bge_pcr_free", "limber_multiplexing", "illumina_htp_novaseqx_paired_end_sequencing"] + request_type_keys: ["limber_bge_pcr_free", "limber_multiplexing"] Limber-Htp - BGE ISC: name: "Limber-Htp - BGE ISC " submission_class_name: "AutomatedOrder" @@ -13,7 +13,7 @@ Limber-Htp - BGE ISC: product_line_name: Illumina-HTP product_catalogue_name: ISC request_type_keys: ["limber_bge_isc", "limber_multiplexing", "illumina_htp_novaseqx_paired_end_sequencing"] # Other request types? -Limber-Htp - BGE Transition: +Limber-Htp - BGE Transition - Automated: name: "Limber-Htp - BGE Transition " submission_class_name: "AutomatedOrder" related_records: From dd2f39e232820db3586d757eb1a8499175c6d87d Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Mon, 25 Nov 2024 15:20:35 +0000 Subject: [PATCH 07/23] Adding product catalogue --- .../product_catalogues/020_bge.wip.yml | 3 +++ .../020_limber_high_throughput_bge.wip.yml | 6 +++--- .../submission_templates/016_bge.wip.yml | 14 +++++++------- 3 files changed, 13 insertions(+), 10 deletions(-) create mode 100644 config/default_records/product_catalogues/020_bge.wip.yml diff --git a/config/default_records/product_catalogues/020_bge.wip.yml b/config/default_records/product_catalogues/020_bge.wip.yml new file mode 100644 index 0000000000..3876dadf46 --- /dev/null +++ b/config/default_records/product_catalogues/020_bge.wip.yml @@ -0,0 +1,3 @@ +--- +BGE: + selection_behaviour: SingleProduct diff --git a/config/default_records/request_types/020_limber_high_throughput_bge.wip.yml b/config/default_records/request_types/020_limber_high_throughput_bge.wip.yml index a955171896..4ae12cff12 100644 --- a/config/default_records/request_types/020_limber_high_throughput_bge.wip.yml +++ b/config/default_records/request_types/020_limber_high_throughput_bge.wip.yml @@ -8,7 +8,7 @@ limber_bge_pcr_free: product_line_name: Illumina-HTP name: Limber BGE PCR Free acceptable_purposes: - - PF Cherrypicked + - BGE Cherrypick library_types: - BGE # For moving PCR Free plates to ISC plates @@ -21,7 +21,7 @@ limber_bge_transition: name: Limber BGE Transition request_class_name: IlluminaHtp::Requests::StdLibraryRequest acceptable_purposes: - - LB Cherrypick + - BGE Lib XP2 library_types: - BGE limber_bge_isc: @@ -32,6 +32,6 @@ limber_bge_isc: name: Limber BGE ISC request_class_name: Pulldown::Requests::IscLibraryRequest acceptable_purposes: - - LB Cherrypick + - BGE Lib PCR XP library_types: - BGE diff --git a/config/default_records/submission_templates/016_bge.wip.yml b/config/default_records/submission_templates/016_bge.wip.yml index ffeb2eb7dc..63ec44e08c 100644 --- a/config/default_records/submission_templates/016_bge.wip.yml +++ b/config/default_records/submission_templates/016_bge.wip.yml @@ -1,22 +1,22 @@ # Y24-366 Limber-Htp - BGE PCR Free: - name: "Limber-Htp - GBE PCR Free" + name: "Limber-Htp - BGE PCR Free" submission_class_name: "LinearSubmission" related_records: product_line_name: Illumina-HTP - product_catalogue_name: PFHSqX + product_catalogue_name: BGE request_type_keys: ["limber_bge_pcr_free", "limber_multiplexing"] Limber-Htp - BGE ISC: - name: "Limber-Htp - BGE ISC " - submission_class_name: "AutomatedOrder" + name: "Limber-Htp - BGE ISC" + submission_class_name: "LinearSubmission" related_records: product_line_name: Illumina-HTP - product_catalogue_name: ISC + product_catalogue_name: BGE request_type_keys: ["limber_bge_isc", "limber_multiplexing", "illumina_htp_novaseqx_paired_end_sequencing"] # Other request types? Limber-Htp - BGE Transition - Automated: - name: "Limber-Htp - BGE Transition " + name: "Limber-Htp - BGE Transition - Automated" submission_class_name: "AutomatedOrder" related_records: product_line_name: Illumina-HTP - product_catalogue_name: ISC # Different product catalogue? + product_catalogue_name: BGE request_type_keys: ["limber_bge_transition"] # Other request types? From 67a91a7596c55ce3aa9f757e219109d71fee13ad Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Mon, 25 Nov 2024 15:38:06 +0000 Subject: [PATCH 08/23] Adding plate purpose BGE --- config/default_records/plate_purposes/014_bge.wip.yml | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 config/default_records/plate_purposes/014_bge.wip.yml diff --git a/config/default_records/plate_purposes/014_bge.wip.yml b/config/default_records/plate_purposes/014_bge.wip.yml new file mode 100644 index 0000000000..78935748c9 --- /dev/null +++ b/config/default_records/plate_purposes/014_bge.wip.yml @@ -0,0 +1,9 @@ +# Plate purposes for BGE +--- +BGE Cherrypick: + type: PlatePurpose::Input + target_type: Plate + stock_plate: true + default_state: passed + cherrypickable_target: true + size: 96 \ No newline at end of file From 24b848f8a1bf82d15f79c7738c547cc8fcf30a69 Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Mon, 25 Nov 2024 15:41:13 +0000 Subject: [PATCH 09/23] Making prettier happy --- config/default_records/plate_purposes/014_bge.wip.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/default_records/plate_purposes/014_bge.wip.yml b/config/default_records/plate_purposes/014_bge.wip.yml index 78935748c9..4bca6b6464 100644 --- a/config/default_records/plate_purposes/014_bge.wip.yml +++ b/config/default_records/plate_purposes/014_bge.wip.yml @@ -6,4 +6,4 @@ BGE Cherrypick: stock_plate: true default_state: passed cherrypickable_target: true - size: 96 \ No newline at end of file + size: 96 From 2c79f2bbc8b16d55134f45d44854e3e81c34780a Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Mon, 25 Nov 2024 15:49:38 +0000 Subject: [PATCH 10/23] Adding the missing plate purpose configs --- .../default_records/plate_purposes/014_bge.wip.yml | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/config/default_records/plate_purposes/014_bge.wip.yml b/config/default_records/plate_purposes/014_bge.wip.yml index 4bca6b6464..fe21322e99 100644 --- a/config/default_records/plate_purposes/014_bge.wip.yml +++ b/config/default_records/plate_purposes/014_bge.wip.yml @@ -7,3 +7,17 @@ BGE Cherrypick: default_state: passed cherrypickable_target: true size: 96 +BGE Lib XP2: + type: PlatePurpose::Input + target_type: Plate + stock_plate: true + default_state: passed + cherrypickable_target: true + size: 96 +BGE Lib PCR XP: + type: PlatePurpose::Input + target_type: Plate + stock_plate: true + default_state: passed + cherrypickable_target: true + size: 96 From 90fb54f44d5eddbb9e0565d53d49b1bba6bfef61 Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Tue, 26 Nov 2024 12:54:09 +0000 Subject: [PATCH 11/23] Updating plate purposes config --- config/default_records/plate_purposes/014_bge.wip.yml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/config/default_records/plate_purposes/014_bge.wip.yml b/config/default_records/plate_purposes/014_bge.wip.yml index fe21322e99..3bf656f394 100644 --- a/config/default_records/plate_purposes/014_bge.wip.yml +++ b/config/default_records/plate_purposes/014_bge.wip.yml @@ -3,21 +3,16 @@ BGE Cherrypick: type: PlatePurpose::Input target_type: Plate - stock_plate: true default_state: passed cherrypickable_target: true size: 96 BGE Lib XP2: - type: PlatePurpose::Input target_type: Plate - stock_plate: true default_state: passed cherrypickable_target: true size: 96 BGE Lib PCR XP: - type: PlatePurpose::Input target_type: Plate - stock_plate: true default_state: passed cherrypickable_target: true size: 96 From 09778cc1c789caed5427b66027d590e916126c39 Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Tue, 26 Nov 2024 13:17:32 +0000 Subject: [PATCH 12/23] Updating plate purposes config --- config/default_records/plate_purposes/014_bge.wip.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/config/default_records/plate_purposes/014_bge.wip.yml b/config/default_records/plate_purposes/014_bge.wip.yml index 3bf656f394..a305778fb8 100644 --- a/config/default_records/plate_purposes/014_bge.wip.yml +++ b/config/default_records/plate_purposes/014_bge.wip.yml @@ -4,15 +4,18 @@ BGE Cherrypick: type: PlatePurpose::Input target_type: Plate default_state: passed + stock_plate: false cherrypickable_target: true size: 96 BGE Lib XP2: target_type: Plate default_state: passed + stock_plate: false cherrypickable_target: true size: 96 BGE Lib PCR XP: target_type: Plate default_state: passed cherrypickable_target: true + stock_plate: false size: 96 From 459f9c0dd32636669b9de5f608d5c061daa7a568 Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Wed, 27 Nov 2024 08:00:47 +0000 Subject: [PATCH 13/23] Unwipping y24-335 --- ..._throughput_hic.wip.yml => 019_limber_high_throughput_hic.yml} | 0 ...eqx_hic_sequencing.wip.yml => 015_novaseqx_hic_sequencing.yml} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename config/default_records/request_types/{019_limber_high_throughput_hic.wip.yml => 019_limber_high_throughput_hic.yml} (100%) rename config/default_records/submission_templates/{015_novaseqx_hic_sequencing.wip.yml => 015_novaseqx_hic_sequencing.yml} (100%) diff --git a/config/default_records/request_types/019_limber_high_throughput_hic.wip.yml b/config/default_records/request_types/019_limber_high_throughput_hic.yml similarity index 100% rename from config/default_records/request_types/019_limber_high_throughput_hic.wip.yml rename to config/default_records/request_types/019_limber_high_throughput_hic.yml diff --git a/config/default_records/submission_templates/015_novaseqx_hic_sequencing.wip.yml b/config/default_records/submission_templates/015_novaseqx_hic_sequencing.yml similarity index 100% rename from config/default_records/submission_templates/015_novaseqx_hic_sequencing.wip.yml rename to config/default_records/submission_templates/015_novaseqx_hic_sequencing.yml From 5b69234a35c80b4c3661cc2f7300a664a9abeb57 Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Wed, 27 Nov 2024 08:08:55 +0000 Subject: [PATCH 14/23] Updating the cherrypickable_target in plates other than cherrypick. --- config/default_records/plate_purposes/014_bge.wip.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/config/default_records/plate_purposes/014_bge.wip.yml b/config/default_records/plate_purposes/014_bge.wip.yml index a305778fb8..9b0e6a16ea 100644 --- a/config/default_records/plate_purposes/014_bge.wip.yml +++ b/config/default_records/plate_purposes/014_bge.wip.yml @@ -11,11 +11,9 @@ BGE Lib XP2: target_type: Plate default_state: passed stock_plate: false - cherrypickable_target: true size: 96 BGE Lib PCR XP: target_type: Plate default_state: passed - cherrypickable_target: true stock_plate: false size: 96 From 9062daeb9aea0e9a2951607101bef338b72c8211 Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Wed, 27 Nov 2024 14:58:12 +0000 Subject: [PATCH 15/23] Removing default_sate for plates other than input plates --- config/default_records/plate_purposes/014_bge.wip.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/config/default_records/plate_purposes/014_bge.wip.yml b/config/default_records/plate_purposes/014_bge.wip.yml index 9b0e6a16ea..4b51f7b5d1 100644 --- a/config/default_records/plate_purposes/014_bge.wip.yml +++ b/config/default_records/plate_purposes/014_bge.wip.yml @@ -9,11 +9,9 @@ BGE Cherrypick: size: 96 BGE Lib XP2: target_type: Plate - default_state: passed stock_plate: false size: 96 BGE Lib PCR XP: target_type: Plate - default_state: passed stock_plate: false size: 96 From fe7240b4dedf711974944b0d51b4f9207d2ad536 Mon Sep 17 00:00:00 2001 From: Katy Taylor Date: Mon, 2 Dec 2024 09:02:43 +0000 Subject: [PATCH 16/23] Change number of samples per pool to allow for larger pools, based on predicted samples coming through --- config/sample_manifest_excel/manifest_types.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/sample_manifest_excel/manifest_types.yml b/config/sample_manifest_excel/manifest_types.yml index 919f7fd337..8eb93c66bc 100644 --- a/config/sample_manifest_excel/manifest_types.yml +++ b/config/sample_manifest_excel/manifest_types.yml @@ -337,7 +337,7 @@ plate_anospp: plate_scrna_core_pools: heading: "scRNA Core Pools Plate" asset_type: "plate" - rows_per_well: 20 + rows_per_well: 120 columns: - :sanger_plate_id - :well From 50c782cd61837421e51b34b91581daba8890937e Mon Sep 17 00:00:00 2001 From: yoldas Date: Mon, 2 Dec 2024 22:14:21 +0000 Subject: [PATCH 17/23] Change library type to emSEQ to maintain consistency with the manual EMseq work done up to now --- .../request_types/018_limber_lcm_triomics_request_types.wip.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/default_records/request_types/018_limber_lcm_triomics_request_types.wip.yml b/config/default_records/request_types/018_limber_lcm_triomics_request_types.wip.yml index 48d9350b7e..e29f215a69 100644 --- a/config/default_records/request_types/018_limber_lcm_triomics_request_types.wip.yml +++ b/config/default_records/request_types/018_limber_lcm_triomics_request_types.wip.yml @@ -11,7 +11,7 @@ limber_lcm_triomics_emseq: acceptable_purposes: - LCMT Lysate library_types: - - LCM Triomics EMSeq + - emSEQ limber_lcm_triomics_wgs: name: LCM Triomics WGS asset_type: Well From a729f4e61fa3a2dbb3270f84b71ca31d7f42c5ae Mon Sep 17 00:00:00 2001 From: yoldas Date: Mon, 2 Dec 2024 22:16:33 +0000 Subject: [PATCH 18/23] Change library type to LCMB as it was being used for the WGS libraries that have recently been submitted for sequencing after manual EMseq library preparation --- .../request_types/018_limber_lcm_triomics_request_types.wip.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/default_records/request_types/018_limber_lcm_triomics_request_types.wip.yml b/config/default_records/request_types/018_limber_lcm_triomics_request_types.wip.yml index e29f215a69..cdc3f13ce4 100644 --- a/config/default_records/request_types/018_limber_lcm_triomics_request_types.wip.yml +++ b/config/default_records/request_types/018_limber_lcm_triomics_request_types.wip.yml @@ -23,4 +23,4 @@ limber_lcm_triomics_wgs: acceptable_purposes: - LCMT DNA Adp Lig library_types: - - LCM Triomics WGS + - LCMB From 24971a1041725e33a22057a3d2d1bea8401f1cca Mon Sep 17 00:00:00 2001 From: Katy Taylor Date: Tue, 3 Dec 2024 11:54:07 +0000 Subject: [PATCH 19/23] Add additional columns to manifest - at request of SSRs --- config/sample_manifest_excel/manifest_types.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/config/sample_manifest_excel/manifest_types.yml b/config/sample_manifest_excel/manifest_types.yml index 8eb93c66bc..72911fb955 100644 --- a/config/sample_manifest_excel/manifest_types.yml +++ b/config/sample_manifest_excel/manifest_types.yml @@ -344,6 +344,11 @@ plate_scrna_core_pools: - :sanger_sample_id - :supplier_name - :donor_id_mandatory + - :date_of_sample_collection + - :country_of_origin + - :gender + - :phenotype + - :sample_ebi_accession_number tube_default: heading: "Default Tube" asset_type: "1dtube" From d574fec4dcae57390cd55d5e912bfd75b3605319 Mon Sep 17 00:00:00 2001 From: Katy Taylor Date: Tue, 3 Dec 2024 14:51:15 +0000 Subject: [PATCH 20/23] add a couple more columns needed for accessioning and push up the number of rows per sample to be safe --- config/sample_manifest_excel/manifest_types.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/config/sample_manifest_excel/manifest_types.yml b/config/sample_manifest_excel/manifest_types.yml index 72911fb955..2c8b49fa1f 100644 --- a/config/sample_manifest_excel/manifest_types.yml +++ b/config/sample_manifest_excel/manifest_types.yml @@ -337,7 +337,7 @@ plate_anospp: plate_scrna_core_pools: heading: "scRNA Core Pools Plate" asset_type: "plate" - rows_per_well: 120 + rows_per_well: 150 columns: - :sanger_plate_id - :well @@ -349,6 +349,8 @@ plate_scrna_core_pools: - :gender - :phenotype - :sample_ebi_accession_number + - :sample_taxon_id + - :sample_common_name tube_default: heading: "Default Tube" asset_type: "1dtube" From 4ed56ca0c2413862c2c0d5e37a96a04f6fb9fab1 Mon Sep 17 00:00:00 2001 From: Katy Taylor Date: Tue, 3 Dec 2024 14:54:51 +0000 Subject: [PATCH 21/23] add explanatory comment --- config/sample_manifest_excel/manifest_types.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/sample_manifest_excel/manifest_types.yml b/config/sample_manifest_excel/manifest_types.yml index 2c8b49fa1f..6e601753ce 100644 --- a/config/sample_manifest_excel/manifest_types.yml +++ b/config/sample_manifest_excel/manifest_types.yml @@ -337,7 +337,7 @@ plate_anospp: plate_scrna_core_pools: heading: "scRNA Core Pools Plate" asset_type: "plate" - rows_per_well: 150 + rows_per_well: 150 # this is a guess at the largest number of samples that will be pooled together columns: - :sanger_plate_id - :well From 4d1c45ed3cf2608a8190ef69dfde177b8902428c Mon Sep 17 00:00:00 2001 From: Katy Taylor Date: Wed, 4 Dec 2024 12:11:47 +0000 Subject: [PATCH 22/23] bump release version --- .release-version | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.release-version b/.release-version index e7e5f7a32f..c7c7493307 100644 --- a/.release-version +++ b/.release-version @@ -1 +1 @@ -14.50.0 +14.50.1 From a3a5863dd76074e5b3a6a8303e836b08ebcec50e Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Mon, 9 Dec 2024 16:40:36 +0530 Subject: [PATCH 23/23] Update .release-version --- .release-version | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.release-version b/.release-version index c7c7493307..379e3d4117 100644 --- a/.release-version +++ b/.release-version @@ -1 +1 @@ -14.50.1 +14.51.0