Merge pull request #56 from kids-first/feature/refactor-lupo

🛠️ refactor/rename Lupo study to new ID

STUDY_CONFIGS/aml_sd_z6mwd3h0_2018_case_meta_config.json → STUDY_CONFIGS/bllnos_sd_z6mwd3h0_2018_case_meta_config.json

@@ -120,7 +120,7 @@
         "_comment": "see https://docs.cbioportal.org/5.1-data-loading/data-loading/file-formats#cancer-study for detailed specifics",
         "description": "Children with Down syndrome (DS), which occurs due to trisomy 21, have a 2000-fold increased risk of atrioventricular septal defects (AVSD) and a 20-fold increased risk of acute lymphoblastic leukemia (ALL), but it is not understood which genetic features of trisomy 21 are responsible for the increased risk. The objectives of this study are to determine the genetic variants underlying AVSD and ALL risk in children with DS, which builds upon our previous work suggesting having an extra copy of chromosome 21 may \"move\" the susceptibility threshold for disease in these children. Insights into the genes that drive DS-AVSD and DS-ALL may have implications for improved genetic counseling, surveillance, clinical management, and treatment strategies for these and other children who may develop AVSD or ALL. Additional keywords: GMKF, KF. For updates, please see here: <a href=\"https://tinyurl.com/55cxz9am\">Release Notes</a>",
         "groups": "PUBLIC",
-        "cancer_study_identifier": "aml_sd_z6mwd3h0_2018",
+        "cancer_study_identifier": "bllnos_sd_z6mwd3h0_2018",
         "type_of_cancer": "aml",
         "short_name": "Genomic Analysis of CHD and ALL in Children with Down Syndrome",
         "reference_genome": "hg38",
@@ -171,28 +171,28 @@
     "database_pulls": {
         "_comment": "This section is used to numerate relevant database schema and tables needed for clinical data and supporting genomic etl files",
         "manifests": {
-            "aml_sd_z6mwd3h0_2018": {
+            "bllnos_sd_z6mwd3h0_2018": {
                 "table": "bix_genomics_file.sd_z6mwd3h0-genomics_file_manifest",
                 "file_type": ["RSEM_gene","annofuse_filtered_fusions_tsv","annotated_public_outputs","ctrlfreec_pval","ctrlfreec_info","ctrlfreec_bam_seg"],
-                "out_file": "aml_sd_z6mwd3h0_2018_genomics_file_manifest.txt"
+                "out_file": "bllnos_sd_z6mwd3h0_2018_genomics_file_manifest.txt"
             }
         },
         "sample_head": {
             "table": "template_sample_header.txt"
         },
         "sample_file": {
-            "table": "brownm28_dev_schema_cbio.aml_sd_z6mwd3h0_2018_data_clinical_sample",
+            "table": "prod_cbio.bllnos_sd_z6mwd3h0_2018_data_clinical_sample",
             "out_file": "data_clinical_sample.txt"
         },
         "patient_head": {
             "table": "template_patient_header.txt"
         },
         "patient_file": {
-            "table": "brownm28_dev_schema_cbio.aml_sd_z6mwd3h0_2018_data_clinical_patient",
+            "table": "prod_cbio.bllnos_sd_z6mwd3h0_2018_data_clinical_patient",
             "out_file": "data_clinical_patient.txt"
         },
         "genomics_etl": {
-            "table": "brownm28_dev_schema_cbio.aml_sd_z6mwd3h0_2018_genomics_etl_file",
+            "table": "prod_cbio.bllnos_sd_z6mwd3h0_2018_genomics_etl_file",
             "out_file": "cbio_file_name_id.txt"
         }
     }