From df2bf66442eda29092c7332ec6ab114b51df04ab Mon Sep 17 00:00:00 2001 From: ufgauthi Date: Thu, 16 Feb 2023 17:15:22 -0500 Subject: [PATCH 1/2] Removed unused workflows and workflows that need work. Added specification to library conversion. --- backend/fms_core/migrations/0049_v4_0_0.py | 80 ++-------------------- 1 file changed, 4 insertions(+), 76 deletions(-) diff --git a/backend/fms_core/migrations/0049_v4_0_0.py b/backend/fms_core/migrations/0049_v4_0_0.py index 4f4b5d555..e2460a98e 100644 --- a/backend/fms_core/migrations/0049_v4_0_0.py +++ b/backend/fms_core/migrations/0049_v4_0_0.py @@ -76,36 +76,12 @@ def initialize_workflows(apps, schema_editor): {"name": "Library Preparation (WGBS, Illumina)", "protocol_name": "Library Preparation", "specifications": [{"display_name": "Library Type", "sheet_name": "Library Batch", "column_name": "Library Type", "value": "WGBS"}, {"display_name": "Library Platform", "sheet_name": "Library Batch", "column_name": "Platform", "value": "ILLUMINA"},]}, - {"name": "Library Preparation (16S, Illumina)", "protocol_name": "Library Preparation", - "specifications": [{"display_name": "Library Type", "sheet_name": "Library Batch", "column_name": "Library Type", "value": "16S"}, - {"display_name": "Library Platform", "sheet_name": "Library Batch", "column_name": "Platform", "value": "ILLUMINA"},]}, - {"name": "Library Preparation (18S, Illumina)", "protocol_name": "Library Preparation", - "specifications": [{"display_name": "Library Type", "sheet_name": "Library Batch", "column_name": "Library Type", "value": "18S"}, - {"display_name": "Library Platform", "sheet_name": "Library Batch", "column_name": "Platform", "value": "ILLUMINA"},]}, {"name": "Library Preparation (miRNA, Illumina)", "protocol_name": "Library Preparation", "specifications": [{"display_name": "Library Type", "sheet_name": "Library Batch", "column_name": "Library Type", "value": "miRNA"}, {"display_name": "Library Platform", "sheet_name": "Library Batch", "column_name": "Platform", "value": "ILLUMINA"},]}, {"name": "Library Preparation (PCR-free, DNBSEQ)", "protocol_name": "Library Preparation", "specifications": [{"display_name": "Library Type", "sheet_name": "Library Batch", "column_name": "Library Type", "value": "PCR-free"}, {"display_name": "Library Platform", "sheet_name": "Library Batch", "column_name": "Platform", "value": "DNBSEQ"},]}, - {"name": "Library Preparation (PCR-enriched, DNBSEQ)", "protocol_name": "Library Preparation", - "specifications": [{"display_name": "Library Type", "sheet_name": "Library Batch", "column_name": "Library Type", "value": "PCR-enriched"}, - {"display_name": "Library Platform", "sheet_name": "Library Batch", "column_name": "Platform", "value": "DNBSEQ"},]}, - {"name": "Library Preparation (RNASeq, DNBSEQ)", "protocol_name": "Library Preparation", - "specifications": [{"display_name": "Library Type", "sheet_name": "Library Batch", "column_name": "Library Type", "value": "RNASeq"}, - {"display_name": "Library Platform", "sheet_name": "Library Batch", "column_name": "Platform", "value": "DNBSEQ"},]}, - {"name": "Library Preparation (WGBS, DNBSEQ)", "protocol_name": "Library Preparation", - "specifications": [{"display_name": "Library Type", "sheet_name": "Library Batch", "column_name": "Library Type", "value": "WGBS"}, - {"display_name": "Library Platform", "sheet_name": "Library Batch", "column_name": "Platform", "value": "DNBSEQ"},]}, - {"name": "Library Preparation (16S, DNBSEQ)", "protocol_name": "Library Preparation", - "specifications": [{"display_name": "Library Type", "sheet_name": "Library Batch", "column_name": "Library Type", "value": "16S"}, - {"display_name": "Library Platform", "sheet_name": "Library Batch", "column_name": "Platform", "value": "DNBSEQ"},]}, - {"name": "Library Preparation (18S, DNBSEQ)", "protocol_name": "Library Preparation", - "specifications": [{"display_name": "Library Type", "sheet_name": "Library Batch", "column_name": "Library Type", "value": "18S"}, - {"display_name": "Library Platform", "sheet_name": "Library Batch", "column_name": "Platform", "value": "DNBSEQ"},]}, - {"name": "Library Preparation (miRNA, DNBSEQ)", "protocol_name": "Library Preparation", - "specifications": [{"display_name": "Library Type", "sheet_name": "Library Batch", "column_name": "Library Type", "value": "miRNA"}, - {"display_name": "Library Platform", "sheet_name": "Library Batch", "column_name": "Platform", "value": "DNBSEQ"},]}, {"name": "Library QC", "protocol_name": "Library Quality Control", "specifications": []}, {"name": "Pooling", "protocol_name": "Sample Pooling", @@ -114,8 +90,8 @@ def initialize_workflows(apps, schema_editor): "specifications": []}, {"name": "Experiment Run DNBSEQ", "protocol_name": "DNBSEQ Preparation", "specifications": []}, - {"name": "Library Conversion", "protocol_name": "Library Conversion", - "specifications": []}, + {"name": "Library Conversion (DNBSEQ)", "protocol_name": "Library Conversion", + "specifications": [{"display_name": "New Library Platform", "sheet_name": "Conversion Batch", "column_name": "Platform", "value": "DNBSEQ"}]}, {"name": "Library Capture (MCC)", "protocol_name": "Library Capture", "specifications": [{"display_name": "Capture Type", "sheet_name": "Capture Batch", "column_name": "Capture Type", "value": "MCC"}]}, {"name": "Library Capture (Exome)", "protocol_name": "Library Capture", @@ -132,65 +108,17 @@ def initialize_workflows(apps, schema_editor): ("WGBS Illumina", "Basic Illumina", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (WGBS, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), ("RNASeq Illumina", "Basic Illumina", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (RNASeq, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), ("miRNA Illumina", "Basic Illumina", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (miRNA, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - ("16S Illumina", "Basic Illumina", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (16S, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - ("18S Illumina", "Basic Illumina", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (18S, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), # Basic DNBSEQ ("PCR-free DNBSEQ", "Basic DNBSEQ", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (PCR-free, DNBSEQ)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run DNBSEQ"]), - # Conversion to DNBSEQ - ("PCR-enriched Conversion DNBSEQ", "Conversion to DNBSEQ", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (PCR-enriched, Illumina)", "Library QC", "Library Conversion", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run DNBSEQ"]), - ("WGBS Conversion DNBSEQ", "Conversion to DNBSEQ", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (WGBS, Illumina)", "Library QC", "Library Conversion", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run DNBSEQ"]), - ("RNASeq Conversion DNBSEQ", "Conversion to DNBSEQ", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (RNASeq, Illumina)", "Library QC", "Library Conversion", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run DNBSEQ"]), - ("miRNA Conversion DNBSEQ", "Conversion to DNBSEQ", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (miRNA, Illumina)", "Library QC", "Library Conversion", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run DNBSEQ"]), - ("16S Conversion DNBSEQ", "Conversion to DNBSEQ", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (16S, Illumina)", "Library QC", "Library Conversion", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run DNBSEQ"]), - ("18S Conversion DNBSEQ", "Conversion to DNBSEQ", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (18S, Illumina)", "Library QC", "Library Conversion", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run DNBSEQ"]), # Capture Illumina - ("PCR-free Capture MCC Illumina", "Capture Illumina", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (PCR-free, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (MCC)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - ("PCR-free Capture Exome Illumina", "Capture Illumina", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (PCR-free, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Exome)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), ("PCR-free Capture Panel Illumina", "Capture Illumina", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (PCR-free, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Panel)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - ("PCR-enriched Capture MCC Illumina", "Capture Illumina", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (PCR-enriched, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (MCC)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), ("PCR-enriched Capture Exome Illumina", "Capture Illumina", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (PCR-enriched, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Exome)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), ("PCR-enriched Capture Panel Illumina", "Capture Illumina", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (PCR-enriched, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Panel)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), ("WGBS Capture MCC Illumina", "Capture Illumina", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (WGBS, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (MCC)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - ("WGBS Capture Exome Illumina", "Capture Illumina", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (WGBS, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Exome)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - ("WGBS Capture Panel Illumina", "Capture Illumina", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (WGBS, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Panel)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - ("RNASeq Capture MCC Illumina", "Capture Illumina", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (RNASeq, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (MCC)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - ("RNASeq Capture Exome Illumina", "Capture Illumina", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (RNASeq, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Exome)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - ("RNASeq Capture Panel Illumina", "Capture Illumina", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (RNASeq, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Panel)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - ("miRNA Capture MCC Illumina", "Capture Illumina", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (miRNA, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (MCC)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - ("miRNA Capture Exome Illumina", "Capture Illumina", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (miRNA, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Exome)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - ("miRNA Capture Panel Illumina", "Capture Illumina", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (miRNA, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Panel)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - ("16S Capture MCC Illumina", "Capture Illumina", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (16S, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (MCC)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - ("16S Capture Exome Illumina", "Capture Illumina", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (16S, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Exome)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - ("16S Capture Panel Illumina", "Capture Illumina", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (16S, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Panel)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - ("18S Capture MCC Illumina", "Capture Illumina", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (18S, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (MCC)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - ("18S Capture Exome Illumina", "Capture Illumina", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (18S, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Exome)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - ("18S Capture Panel Illumina", "Capture Illumina", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (18S, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Panel)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - # Capture DNBSEQ - ("PCR-free Capture MCC DNBSEQ", "Capture DNBSEQ", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (PCR-free, DNBSEQ)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (MCC)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run DNBSEQ"]), - ("PCR-free Capture Exome DNBSEQ", "Capture DNBSEQ", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (PCR-free, DNBSEQ)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Exome)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run DNBSEQ"]), - ("PCR-free Capture Panel DNBSEQ", "Capture DNBSEQ", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (PCR-free, DNBSEQ)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Panel)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run DNBSEQ"]), - # Capture Conversion to DNBSEQ - ("PCR-enriched Capture MCC Conversion DNBSEQ", "Capture Conversion to DNBSEQ", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (PCR-enriched, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (MCC)", "Library QC", "Normalization (Library)", "Pooling", "Library Conversion", "Library QC", "Experiment Run DNBSEQ"]), - ("PCR-enriched Capture Exome Conversion DNBSEQ", "Capture Conversion to DNBSEQ", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (PCR-enriched, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Exome)", "Library QC", "Normalization (Library)", "Pooling", "Library Conversion", "Library QC", "Experiment Run DNBSEQ"]), - ("PCR-enriched Capture Panel Conversion DNBSEQ", "Capture Conversion to DNBSEQ", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (PCR-enriched, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Panel)", "Library QC", "Normalization (Library)", "Pooling", "Library Conversion", "Library QC", "Experiment Run DNBSEQ"]), - ("WGBS Capture MCC Conversion DNBSEQ", "Capture Conversion to DNBSEQ", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (WGBS, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (MCC)", "Library QC", "Normalization (Library)", "Pooling", "Library Conversion", "Library QC", "Experiment Run DNBSEQ"]), - ("WGBS Capture Exome Conversion DNBSEQ", "Capture Conversion to DNBSEQ", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (WGBS, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Exome)", "Library QC", "Normalization (Library)", "Pooling", "Library Conversion", "Library QC", "Experiment Run DNBSEQ"]), - ("WGBS Capture Panel Conversion DNBSEQ", "Capture Conversion to DNBSEQ", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (WGBS, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Panel)", "Library QC", "Normalization (Library)", "Pooling", "Library Conversion", "Library QC", "Experiment Run DNBSEQ"]), - ("RNASeq Capture MCC Conversion DNBSEQ", "Capture Conversion to DNBSEQ", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (RNASeq, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (MCC)", "Library QC", "Normalization (Library)", "Pooling", "Library Conversion", "Library QC", "Experiment Run DNBSEQ"]), - ("RNASeq Capture Exome Conversion DNBSEQ", "Capture Conversion to DNBSEQ", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (RNASeq, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Exome)", "Library QC", "Normalization (Library)", "Pooling", "Library Conversion", "Library QC", "Experiment Run DNBSEQ"]), - ("RNASeq Capture Panel Conversion DNBSEQ", "Capture Conversion to DNBSEQ", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (RNASeq, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Panel)", "Library QC", "Normalization (Library)", "Pooling", "Library Conversion", "Library QC", "Experiment Run DNBSEQ"]), - ("miRNA Capture MCC Conversion DNBSEQ", "Capture Conversion to DNBSEQ", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (miRNA, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (MCC)", "Library QC", "Normalization (Library)", "Pooling", "Library Conversion", "Library QC", "Experiment Run DNBSEQ"]), - ("miRNA Capture Exome Conversion DNBSEQ", "Capture Conversion to DNBSEQ", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (miRNA, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Exome)", "Library QC", "Normalization (Library)", "Pooling", "Library Conversion", "Library QC", "Experiment Run DNBSEQ"]), - ("miRNA Capture Panel Conversion DNBSEQ", "Capture Conversion to DNBSEQ", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (miRNA, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Panel)", "Library QC", "Normalization (Library)", "Pooling", "Library Conversion", "Library QC", "Experiment Run DNBSEQ"]), - ("16S Capture MCC Conversion DNBSEQ", "Capture Conversion to DNBSEQ", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (16S, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (MCC)", "Library QC", "Normalization (Library)", "Pooling", "Library Conversion", "Library QC", "Experiment Run DNBSEQ"]), - ("16S Capture Exome Conversion DNBSEQ", "Capture Conversion to DNBSEQ", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (16S, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Exome)", "Library QC", "Normalization (Library)", "Pooling", "Library Conversion", "Library QC", "Experiment Run DNBSEQ"]), - ("16S Capture Panel Conversion DNBSEQ", "Capture Conversion to DNBSEQ", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (16S, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Panel)", "Library QC", "Normalization (Library)", "Pooling", "Library Conversion", "Library QC", "Experiment Run DNBSEQ"]), - ("18S Capture MCC Conversion DNBSEQ", "Capture Conversion to DNBSEQ", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (18S, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (MCC)", "Library QC", "Normalization (Library)", "Pooling", "Library Conversion", "Library QC", "Experiment Run DNBSEQ"]), - ("18S Capture Exome Conversion DNBSEQ", "Capture Conversion to DNBSEQ", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (18S, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Exome)", "Library QC", "Normalization (Library)", "Pooling", "Library Conversion", "Library QC", "Experiment Run DNBSEQ"]), - ("18S Capture Panel Conversion DNBSEQ", "Capture Conversion to DNBSEQ", ["Extraction (RNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (18S, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Panel)", "Library QC", "Normalization (Library)", "Pooling", "Library Conversion", "Library QC", "Experiment Run DNBSEQ"]), # Ready-to-Sequence ("Ready-to-Sequence Illumina", "Ready-to-Sequence", ["Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - ("Ready-to-Sequence DNBSEQ", "Ready-to-Sequence", ["Library QC", "Normalization (Library)", "Pooling", "Experiment Run DNBSEQ"]) + # Ready-to-Sequence Conversion + ("Ready-to-Sequence Conversion DNBSEQ", "Ready-to-Sequence Conversion", ["Library QC", "Library Conversion (DNBSEQ)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run DNBSEQ"]) ] with reversion.create_revision(manage_manually=True): From 1883f9f016dc024a3536347ca84baffd0fc06c91 Mon Sep 17 00:00:00 2001 From: ufgauthi Date: Mon, 20 Feb 2023 11:12:22 -0500 Subject: [PATCH 2/2] removed panel capture workflows --- backend/fms_core/migrations/0049_v4_0_0.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/backend/fms_core/migrations/0049_v4_0_0.py b/backend/fms_core/migrations/0049_v4_0_0.py index e2460a98e..c27c28820 100644 --- a/backend/fms_core/migrations/0049_v4_0_0.py +++ b/backend/fms_core/migrations/0049_v4_0_0.py @@ -96,8 +96,6 @@ def initialize_workflows(apps, schema_editor): "specifications": [{"display_name": "Capture Type", "sheet_name": "Capture Batch", "column_name": "Capture Type", "value": "MCC"}]}, {"name": "Library Capture (Exome)", "protocol_name": "Library Capture", "specifications": [{"display_name": "Capture Type", "sheet_name": "Capture Batch", "column_name": "Capture Type", "value": "Exome"}]}, - {"name": "Library Capture (Panel)", "protocol_name": "Library Capture", - "specifications": [{"display_name": "Capture Type", "sheet_name": "Capture Batch", "column_name": "Capture Type", "value": "Panel"}]}, ] WORKFLOWS = [ @@ -111,9 +109,7 @@ def initialize_workflows(apps, schema_editor): # Basic DNBSEQ ("PCR-free DNBSEQ", "Basic DNBSEQ", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (PCR-free, DNBSEQ)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run DNBSEQ"]), # Capture Illumina - ("PCR-free Capture Panel Illumina", "Capture Illumina", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (PCR-free, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Panel)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), ("PCR-enriched Capture Exome Illumina", "Capture Illumina", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (PCR-enriched, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Exome)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), - ("PCR-enriched Capture Panel Illumina", "Capture Illumina", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (PCR-enriched, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (Panel)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), ("WGBS Capture MCC Illumina", "Capture Illumina", ["Extraction (DNA)", "Sample QC", "Normalization (Sample)", "Library Preparation (WGBS, Illumina)", "Library QC", "Normalization (Library)", "Pooling", "Library Capture (MCC)", "Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]), # Ready-to-Sequence ("Ready-to-Sequence Illumina", "Ready-to-Sequence", ["Library QC", "Normalization (Library)", "Pooling", "Experiment Run Illumina"]),