🔨 updated mioncoseq to pull from more studies

📝 corrected a rampant typo
kids-first · Jan 10, 2024 · c4db157 · c4db157
1 parent 9bc0e3f
commit c4db157
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Showing 19 changed files with 47 additions and 37 deletions.
diff --git a/COLLABORATIONS/openPBTA/openpbta_case_meta_config.json b/COLLABORATIONS/openPBTA/openpbta_case_meta_config.json
@@ -122,7 +122,7 @@
     },
     "cases_3way_complete": {
         "stable_id": "3way_complete",
-        "case_list_name": "Tumor samples with mutatation, CNA and mRNA data",
+        "case_list_name": "Tumor samples with mutation, CNA and mRNA data",
         "case_list_description": "All tumor samples with mutation, CNA, and mRNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_and_mrna_data"
     },
@@ -134,7 +134,7 @@
     },
     "cases_cnaseq": {
         "stable_id": "cnaseq",
-        "case_list_name": "Tumor samples with mutatation and CNA data",
+        "case_list_name": "Tumor samples with mutation and CNA data",
         "case_list_description": "All tumor samples with mutation and CNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_data"
     },

diff --git a/COLLABORATIONS/openTARGETS/case_openTargets_meta_config.json b/COLLABORATIONS/openTARGETS/case_openTargets_meta_config.json
@@ -125,7 +125,7 @@
     },
     "cases_3way_complete": {
         "stable_id": "3way_complete",
-        "case_list_name": "Tumor samples with mutatation, CNA and mRNA data",
+        "case_list_name": "Tumor samples with mutation, CNA and mRNA data",
         "case_list_description": "All tumor samples with mutation, CNA, and mRNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_and_mrna_data"
     },
@@ -137,7 +137,7 @@
     },
     "cases_cnaseq": {
         "stable_id": "cnaseq",
-        "case_list_name": "Tumor samples with mutatation and CNA data",
+        "case_list_name": "Tumor samples with mutation and CNA data",
         "case_list_description": "All tumor samples with mutation and CNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_data"
     },

diff --git a/COLLABORATIONS/openTARGETS/openpedcan_v11_case_meta_config.json b/COLLABORATIONS/openTARGETS/openpedcan_v11_case_meta_config.json
@@ -135,7 +135,7 @@
     },
     "cases_3way_complete": {
         "stable_id": "3way_complete",
-        "case_list_name": "Tumor samples with mutatation, CNA and mRNA data",
+        "case_list_name": "Tumor samples with mutation, CNA and mRNA data",
         "case_list_description": "All tumor samples with mutation, CNA, and mRNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_and_mrna_data"
     },
@@ -147,7 +147,7 @@
     },
     "cases_cnaseq": {
         "stable_id": "cnaseq",
-        "case_list_name": "Tumor samples with mutatation and CNA data",
+        "case_list_name": "Tumor samples with mutation and CNA data",
         "case_list_description": "All tumor samples with mutation and CNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_data"
     },

diff --git a/COLLABORATIONS/openTARGETS/openpedcan_v12_case_meta_config.json b/COLLABORATIONS/openTARGETS/openpedcan_v12_case_meta_config.json
@@ -126,7 +126,7 @@
     },
     "cases_3way_complete": {
         "stable_id": "3way_complete",
-        "case_list_name": "Tumor samples with mutatation, CNA and mRNA data",
+        "case_list_name": "Tumor samples with mutation, CNA and mRNA data",
         "case_list_description": "All tumor samples with mutation, CNA, and mRNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_and_mrna_data"
     },
@@ -138,7 +138,7 @@
     },
     "cases_cnaseq": {
         "stable_id": "cnaseq",
-        "case_list_name": "Tumor samples with mutatation and CNA data",
+        "case_list_name": "Tumor samples with mutation and CNA data",
         "case_list_description": "All tumor samples with mutation and CNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_data"
     },

diff --git a/PUBLICATIONS/Ijaz_cole/case_Ijaz_cole_published_meta_config.json b/PUBLICATIONS/Ijaz_cole/case_Ijaz_cole_published_meta_config.json
@@ -107,7 +107,7 @@
     },
     "cases_3way_complete": {
         "stable_id": "3way_complete",
-        "case_list_name": "Tumor samples with mutatation, CNA and mRNA data",
+        "case_list_name": "Tumor samples with mutation, CNA and mRNA data",
         "case_list_description": "All tumor samples with mutation, CNA, and mRNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_and_mrna_data"
     },
@@ -120,7 +120,7 @@
     },
     "cases_cnaseq": {
         "stable_id": "cnaseq",
-        "case_list_name": "Tumor samples with mutatation and CNA data",
+        "case_list_name": "Tumor samples with mutation and CNA data",
         "case_list_description": "All tumor samples with mutation and CNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_data"
     },

diff --git a/PUBLICATIONS/cptac_proteomics/case_cptac_published_meta_config.json b/PUBLICATIONS/cptac_proteomics/case_cptac_published_meta_config.json
@@ -122,7 +122,7 @@
     },
     "cases_3way_complete": {
         "stable_id": "3way_complete",
-        "case_list_name": "Tumor samples with mutatation, CNA and mRNA data",
+        "case_list_name": "Tumor samples with mutation, CNA and mRNA data",
         "case_list_description": "All tumor samples with mutation, CNA, and mRNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_and_mrna_data"
     },
@@ -134,7 +134,7 @@
     },
     "cases_cnaseq": {
         "stable_id": "cnaseq",
-        "case_list_name": "Tumor samples with mutatation and CNA data",
+        "case_list_name": "Tumor samples with mutation and CNA data",
         "case_list_description": "All tumor samples with mutation and CNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_data"
     },

diff --git a/STUDY_CONFIGS/aml_sd_z6mwd3h0_2018_case_meta_config.json b/STUDY_CONFIGS/aml_sd_z6mwd3h0_2018_case_meta_config.json
@@ -128,7 +128,7 @@
     },
     "cases_3way_complete": {
         "stable_id": "3way_complete",
-        "case_list_name": "Tumor and model samples with mutatation, CNA and mRNA data",
+        "case_list_name": "Tumor and model samples with mutation, CNA and mRNA data",
         "case_list_description": "All tumor and model samples with mutation, CNA, and mRNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_and_mrna_data"
     },
@@ -140,7 +140,7 @@
     },
     "cases_cnaseq": {
         "stable_id": "cnaseq",
-        "case_list_name": "Tumor samples with mutatation and CNA data",
+        "case_list_name": "Tumor samples with mutation and CNA data",
         "case_list_description": "All tumor samples with mutation and CNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_data"
     },

diff --git a/STUDY_CONFIGS/case_cptac_meta_config.json b/STUDY_CONFIGS/case_cptac_meta_config.json
@@ -121,7 +121,7 @@
     },
     "cases_3way_complete": {
         "stable_id": "3way_complete",
-        "case_list_name": "Tumor samples with mutatation, CNA and mRNA data",
+        "case_list_name": "Tumor samples with mutation, CNA and mRNA data",
         "case_list_description": "All tumor samples with mutation, CNA, and mRNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_and_mrna_data"
     },
@@ -133,7 +133,7 @@
     },
     "cases_cnaseq": {
         "stable_id": "cnaseq",
-        "case_list_name": "Tumor samples with mutatation and CNA data",
+        "case_list_name": "Tumor samples with mutation and CNA data",
         "case_list_description": "All tumor samples with mutation and CNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_data"
     },

diff --git a/STUDY_CONFIGS/chdm_phs001643_2018_case_meta_config.json b/STUDY_CONFIGS/chdm_phs001643_2018_case_meta_config.json
@@ -176,7 +176,7 @@
     },
     "cases_3way_complete": {
         "stable_id": "3way_complete",
-        "case_list_name": "Tumor and model samples with mutatation, CNA and mRNA data",
+        "case_list_name": "Tumor and model samples with mutation, CNA and mRNA data",
         "case_list_description": "All tumor and model samples with mutation, CNA, and mRNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_and_mrna_data"
     },
@@ -188,7 +188,7 @@
     },
     "cases_cnaseq": {
         "stable_id": "cnaseq",
-        "case_list_name": "Tumor samples with mutatation and CNA data",
+        "case_list_name": "Tumor samples with mutation and CNA data",
         "case_list_description": "All tumor samples with mutation and CNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_data"
     },

diff --git a/STUDY_CONFIGS/chdm_phs002301_2021_case_meta_config.json b/STUDY_CONFIGS/chdm_phs002301_2021_case_meta_config.json
@@ -119,7 +119,7 @@
     "study": {
         "_comment": "see https://docs.cbioportal.org/5.1-data-loading/data-loading/file-formats#cancer-study for detailed specifics",
         "description": "Chordoma is a rare bone tumor, which is believed to originate from notochordal remnants. Based on the United States Surveillance Epidemiology and End Results (SEER) data, the incidence of chordoma varies by gender and race; however, little is known about the etiologic factors that predispose to it. Genomic profiling studies of chordoma are limited, particularly in the Chinese population. We therefore conducted a detailed molecular characterization of paired chordoma tumor/normal tissues using fresh frozen tissues and blood collected from skull-based Chinese chordoma patients. These analyses included whole exome sequencing and RNA sequencing analyses. For updates, please see here: <a href=\"https://tinyurl.com/55cxz9am\">Release Notes</a>",
-        "groups": "PUBLIC",
+        "groups": "phs002301",
         "cancer_study_identifier": "chdm_phs002301_2021",
         "type_of_cancer": "chdm",
         "short_name": "chdm_phs002301_2021",

diff --git a/STUDY_CONFIGS/chdm_sd_7spqtt8m_case_meta_config.json b/STUDY_CONFIGS/chdm_sd_7spqtt8m_case_meta_config.json
@@ -176,7 +176,7 @@
     },
     "cases_3way_complete": {
         "stable_id": "3way_complete",
-        "case_list_name": "Tumor and model samples with mutatation, CNA and mRNA data",
+        "case_list_name": "Tumor and model samples with mutation, CNA and mRNA data",
         "case_list_description": "All tumor and model samples with mutation, CNA, and mRNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_and_mrna_data"
     },
@@ -188,7 +188,7 @@
     },
     "cases_cnaseq": {
         "stable_id": "cnaseq",
-        "case_list_name": "Tumor samples with mutatation and CNA data",
+        "case_list_name": "Tumor samples with mutation and CNA data",
         "case_list_description": "All tumor samples with mutation and CNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_data"
     },

diff --git a/STUDY_CONFIGS/oligo_nation_case_meta_config.json b/STUDY_CONFIGS/oligo_nation_case_meta_config.json
@@ -133,7 +133,7 @@
     },
     "cases_3way_complete": {
         "stable_id": "3way_complete",
-        "case_list_name": "Tumor samples with mutatation, CNA and mRNA data",
+        "case_list_name": "Tumor samples with mutation, CNA and mRNA data",
         "case_list_description": "All tumor samples with mutation, CNA, and mRNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_and_mrna_data"
     },
@@ -145,7 +145,7 @@
     },
     "cases_cnaseq": {
         "stable_id": "cnaseq",
-        "case_list_name": "Tumor samples with mutatation and CNA data",
+        "case_list_name": "Tumor samples with mutation and CNA data",
         "case_list_description": "All tumor samples with mutation and CNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_data"
     },

diff --git a/STUDY_CONFIGS/open_chordoma_case_meta_config.json b/STUDY_CONFIGS/open_chordoma_case_meta_config.json
@@ -185,7 +185,7 @@
     },
     "cases_3way_complete": {
         "stable_id": "3way_complete",
-        "case_list_name": "Tumor and model samples with mutatation, CNA and mRNA data",
+        "case_list_name": "Tumor and model samples with mutation, CNA and mRNA data",
         "case_list_description": "All tumor and model samples with mutation, CNA, and mRNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_and_mrna_data"
     },
@@ -197,7 +197,7 @@
     },
     "cases_cnaseq": {
         "stable_id": "cnaseq",
-        "case_list_name": "Tumor samples with mutatation and CNA data",
+        "case_list_name": "Tumor samples with mutation and CNA data",
         "case_list_description": "All tumor samples with mutation and CNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_data"
     },

diff --git a/STUDY_CONFIGS/os_sd_zxjffmef_2015_case_meta_config.json b/STUDY_CONFIGS/os_sd_zxjffmef_2015_case_meta_config.json
@@ -128,7 +128,7 @@
     },
     "cases_3way_complete": {
         "stable_id": "3way_complete",
-        "case_list_name": "Tumor and model samples with mutatation, CNA and mRNA data",
+        "case_list_name": "Tumor and model samples with mutation, CNA and mRNA data",
         "case_list_description": "All tumor and model samples with mutation, CNA, and mRNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_and_mrna_data"
     },
@@ -140,7 +140,7 @@
     },
     "cases_cnaseq": {
         "stable_id": "cnaseq",
-        "case_list_name": "Tumor samples with mutatation and CNA data",
+        "case_list_name": "Tumor samples with mutation and CNA data",
         "case_list_description": "All tumor samples with mutation and CNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_data"
     },

diff --git a/STUDY_CONFIGS/pbta_all_case_meta_config.json b/STUDY_CONFIGS/pbta_all_case_meta_config.json
@@ -176,7 +176,7 @@
     },
     "cases_3way_complete": {
         "stable_id": "3way_complete",
-        "case_list_name": "Tumor samples with mutatation, CNA and mRNA data",
+        "case_list_name": "Tumor samples with mutation, CNA and mRNA data",
         "case_list_description": "All tumor samples with mutation, CNA, and mRNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_and_mrna_data"
     },
@@ -188,7 +188,7 @@
     },
     "cases_cnaseq": {
         "stable_id": "cnaseq",
-        "case_list_name": "Tumor samples with mutatation and CNA data",
+        "case_list_name": "Tumor samples with mutation and CNA data",
         "case_list_description": "All tumor samples with mutation and CNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_data"
     },

diff --git a/STUDY_CONFIGS/pbta_all_treatment_meta_config.json b/STUDY_CONFIGS/pbta_all_treatment_meta_config.json
@@ -185,7 +185,7 @@
     },
     "cases_3way_complete": {
         "stable_id": "3way_complete",
-        "case_list_name": "Tumor samples with mutatation, CNA and mRNA data",
+        "case_list_name": "Tumor samples with mutation, CNA and mRNA data",
         "case_list_description": "All tumor samples with mutation, CNA, and mRNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_and_mrna_data"
     },
@@ -197,7 +197,7 @@
     },
     "cases_cnaseq": {
         "stable_id": "cnaseq",
-        "case_list_name": "Tumor samples with mutatation and CNA data",
+        "case_list_name": "Tumor samples with mutation and CNA data",
         "case_list_description": "All tumor samples with mutation and CNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_data"
     },

diff --git a/STUDY_CONFIGS/pbta_mioncoseq_case_meta_config.json b/STUDY_CONFIGS/pbta_mioncoseq_case_meta_config.json
@@ -178,7 +178,7 @@
     },
     "cases_3way_complete": {
         "stable_id": "3way_complete",
-        "case_list_name": "Tumor samples with mutatation, CNA and mRNA data",
+        "case_list_name": "Tumor samples with mutation, CNA and mRNA data",
         "case_list_description": "All tumor samples with mutation, CNA, and mRNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_and_mrna_data"
     },
@@ -190,7 +190,7 @@
     },
     "cases_cnaseq": {
         "stable_id": "cnaseq",
-        "case_list_name": "Tumor samples with mutatation and CNA data",
+        "case_list_name": "Tumor samples with mutation and CNA data",
         "case_list_description": "All tumor samples with mutation and CNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_data"
     },
@@ -225,6 +225,16 @@
                 "table": "bix_genomics_file.sd_bhjxbdqk_mioncoseq-genomics_file_manifest",
                 "file_type": ["RSEM_gene","annofuse_filtered_fusions_tsv","annotated_public_outputs","ctrlfreec_pval","ctrlfreec_info","ctrlfreec_bam_seg"],
                 "out_file": "mioncoseq_genomics_file_manifest.txt"
+            },
+            "x01": {
+                "table": "bix_genomics_file.sd_bhjxbdqk_x01-genomics_file_manifest",
+                "file_type": ["RSEM_gene","annofuse_filtered_fusions_tsv","annotated_public_outputs","consensus_public_outputs","ctrlfreec_pval","ctrlfreec_info","ctrlfreec_bam_seg"],
+                "out_file": "x01_genomics_file_manifest.txt"
+            },
+            "cbtn_extra": {
+                "table": "bix_genomics_file.sd_bhjxbdqk_x01_extra-genomics_file_manifest",
+                "file_type": ["RSEM_gene","annofuse_filtered_fusions_tsv","annotated_public_outputs","consensus_public_outputs","ctrlfreec_pval","ctrlfreec_info","ctrlfreec_bam_seg"],
+                "out_file": "cbtn_extra_genomics_file_manifest.txt"
             }
         },
         "sample_head": {

diff --git a/STUDY_CONFIGS/tll_sd_aq9kvn5p_2019_case_meta_config.json b/STUDY_CONFIGS/tll_sd_aq9kvn5p_2019_case_meta_config.json
@@ -176,7 +176,7 @@
     },
     "cases_3way_complete": {
         "stable_id": "3way_complete",
-        "case_list_name": "Tumor samples with mutatation, CNA and mRNA data",
+        "case_list_name": "Tumor samples with mutation, CNA and mRNA data",
         "case_list_description": "All tumor samples with mutation, CNA, and mRNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_and_mrna_data"
     },
@@ -188,7 +188,7 @@
     },
     "cases_cnaseq": {
         "stable_id": "cnaseq",
-        "case_list_name": "Tumor samples with mutatation and CNA data",
+        "case_list_name": "Tumor samples with mutation and CNA data",
         "case_list_description": "All tumor samples with mutation and CNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_data"
     },

diff --git a/STUDY_CONFIGS/x01_nbl_16_maris_case_meta_config.json b/STUDY_CONFIGS/x01_nbl_16_maris_case_meta_config.json
@@ -170,7 +170,7 @@
     },
     "cases_3way_complete": {
         "stable_id": "3way_complete",
-        "case_list_name": "Tumor samples with mutatation, CNA and mRNA data",
+        "case_list_name": "Tumor samples with mutation, CNA and mRNA data",
         "case_list_description": "All tumor samples with mutation, CNA, and mRNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_and_mrna_data"
     },
@@ -182,7 +182,7 @@
     },
     "cases_cnaseq": {
         "stable_id": "cnaseq",
-        "case_list_name": "Tumor samples with mutatation and CNA data",
+        "case_list_name": "Tumor samples with mutation and CNA data",
         "case_list_description": "All tumor samples with mutation and CNA data",
         "case_list_category": "all_cases_with_mutation_and_cna_data"
     },