From 9bc0e3f79a3bb362ceb7d21151e3774a6e4c9a8b Mon Sep 17 00:00:00 2001 From: Miguel Brown Date: Mon, 11 Dec 2023 15:52:14 -0500 Subject: [PATCH 1/2] :pencil: created chdm dbgap config --- .../chdm_phs002301_2021_case_meta_config.json | 182 ++++++++++++++++++ 1 file changed, 182 insertions(+) create mode 100644 STUDY_CONFIGS/chdm_phs002301_2021_case_meta_config.json diff --git a/STUDY_CONFIGS/chdm_phs002301_2021_case_meta_config.json b/STUDY_CONFIGS/chdm_phs002301_2021_case_meta_config.json new file mode 100644 index 0000000..4af1cf8 --- /dev/null +++ b/STUDY_CONFIGS/chdm_phs002301_2021_case_meta_config.json @@ -0,0 +1,182 @@ +{ + "_doc":{ + "_description": "This section of the document is meant to help understand the organization of key-value pairs and how it supports the creation of files from https://docs.cbioportal.org/5.1-data-loading/data-loading/file-formats as part of the cBioportal ETL", + "sections": { + "merged_x": { + "_description": "Support information for merged genomic data and supporting meta files. ", + "dir": "output directory for merged results. Should match output dir specified by etl conversion script at run time", + "dtypes": { + "_description": "Data types - cBio defined data types. _comment has link to detailed specifics in each section.", + "ext": "File extension of merged outputs from etl script", + "cbio_name": "cBio output file name - a soft link to the etl output created inside the study directory", + "meta_file_attributes": "Direct key-value paris used by cBio in a meta_x file used to describe data_x files" + } + }, + "study": "Special meta file used to describe the cBio study", + "case_x": "cBio case lists - sample lists describing which samples have mutation data, sv data, cnv data, etc. See https://docs.cbioportal.org/5.1-data-loading/data-loading/file-formats#case-lists for specifics", + "data_sheets": "Clinical patient and sample data as well as gene matrix if panel data present. Distinct from other data_x files in that in contains sample and patient metadata and not genomic data", + "database_pulls": { + "_description": "This section is used to support pulling auto-generated clinical data tables and supporting genomics etl information from the D3b Data Warehouse", + "manifests": { + "": { + "_description": "The key for this field is meant to be a convenient descriptor of what sub-study files derive from, as a cBio study make come from many sources", + "table": "D3b warehouse table name with relevant file info", + "file_types": "Manifests typically contain all possible harmonization outputs. Specifying specific file_type(s) limits to relevant outputs. Exception is annotated_public_output, etl will pull only he maf as vcfs are included in that query.", + "out_file": "Desired output file name" + } + }, + "x_head": "Special header file table for data_clinical(sample/patient). cBio data_clinical headers have 5 header rows, and which columns are used are determined by the x_file table", + "x_file": "sample or patient tables with corresponding metadata at the sample and patient levels", + "genomics_etl": "a helper file with relevant cBio sample names and individual genomic files names for ETL merging", + "seq_center": "only if project has RNA data, a helper file to fill in missing sequencing center information for genomics etl", + "gene_file": "Only if study has panel data, the source information for gene matrix in the data_sheets section" + + } + } + }, + "merged_mafs": { + "_comment": "See https://docs.cbioportal.org/5.1-data-loading/data-loading/file-formats#mutation-data for detailed specifics", + "dir": "merged_mafs", + "dtypes": { + "mutation": { + "ext": "maf", + "cbio_name": "data_mutations_extended.txt", + "meta_file_attr": { + "stable_id": "mutations", + "profile_name": "Mutations", + "profile_description": "For matched T/N sample: consensus calls from strelka2, mutect2, lancet, and VarDict Java. Two or more callers required to pass, < 0.001 frequency in gnomAD, and min read depth 8 in normal sample, unless in a TERT promoter region or in a hotspot region (see https://www.cancerhotspots.org). For tumor/model-only, mutect2 calls with < 0.001 frequency in gnomAD, unless in a hotspot region", + "genetic_alteration_type": "MUTATION_EXTENDED", + "datatype": "MAF", + "variant_classification_filter": "Silent,Intron,3'UTR,3'Flank,5'UTR,IGR,RNA", + "show_profile_in_analysis_tab": "true" + } + } + } + }, + "merged_cnvs": { + "dir": "merged_cnvs", + "dtypes": { + "linear": { + "_comment": "see https://docs.cbioportal.org/5.1-data-loading/data-loading/file-formats#continuous-copy-number-data for detailed specifics", + "ext": "predicted_cnv.txt", + "cbio_name": "data_linear_CNA.txt", + "meta_file_attr": { + "stable_id": "linear_CNA", + "profile_name": "copy-number values", + "profile_description": "Predicted copy number values from WGS (Continuous). Copy number calls obtained using ControlFreeC, filtering calls smaller than 50KB", + "genetic_alteration_type": "COPY_NUMBER_ALTERATION", + "datatype": "CONTINUOUS", + "show_profile_in_analysis_tab": "false" + } + }, + "discrete": { + "_comment": "see https://docs.cbioportal.org/5.1-data-loading/data-loading/file-formats#discrete-copy-number-data for detailed specifics", + "ext": "discrete_cnvs.txt", + "cbio_name": "data_CNA.txt", + "meta_file_attr": { + "stable_id": "cna", + "profile_name": "Binned copy-number values", + "profile_description": "Predicted copy number values from WGS (Discrete). Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification", + "genetic_alteration_type": "COPY_NUMBER_ALTERATION", + "datatype": "DISCRETE", + "show_profile_in_analysis_tab": "true" + } + }, + "segment": { + "_comment": "see https://docs.cbioportal.org/5.1-data-loading/data-loading/file-formats#segmented-data for detailed specifics", + "ext": "merged_seg.txt", + "cbio_name": "data_cna.seg.txt", + "meta_file_attr": { + "description": "Tumor/model-only CNA data (with the exception of some paired T/N)", + "genetic_alteration_type": "COPY_NUMBER_ALTERATION", + "datatype": "SEG", + "reference_genome_id": "hg38" + } + } + } + }, + "data_sheets": { + "dir": "datasheets", + "dtypes": { + "patient": { + "_comment": "see https://docs.cbioportal.org/5.1-data-loading/data-loading/file-formats#example-clinical-header for detailed specifics", + "cbio_name": "data_clinical_patient.txt", + "meta_file_attr": { + "genetic_alteration_type": "CLINICAL", + "datatype": "PATIENT_ATTRIBUTES" + } + }, + "sample": { + "_comment": "see https://docs.cbioportal.org/5.1-data-loading/data-loading/file-formats#clinical-sample-columns for detailed specifics", + "cbio_name": "data_clinical_sample.txt", + "meta_file_attr": { + "genetic_alteration_type": "CLINICAL", + "datatype": "SAMPLE_ATTRIBUTES" + } + } + } + }, + "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: Release Notes", + "groups": "PUBLIC", + "cancer_study_identifier": "chdm_phs002301_2021", + "type_of_cancer": "chdm", + "short_name": "chdm_phs002301_2021", + "reference_genome": "hg38", + "display_name": "Whole Genome Sequencing of Skull-Based Chordoma (phs002301, Provisional)", + "pmid": "PMC7859411" + }, + "cases_all": { + "stable_id": "all", + "case_list_name": "All Tumors and models", + "case_list_description": "All tumor and model samples", + "case_list_category": "all_cases_in_study" + }, + "cases_cnaseq": { + "stable_id": "cnaseq", + "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" + }, + "cases_cna": { + "stable_id": "cna", + "case_list_name": "Tumor and model Samples with CNA data", + "case_list_description": "All tumors and models with CNA data", + "case_list_category": "all_cases_with_cna_data" + }, + "cases_sequenced": { + "stable_id": "sequenced", + "case_list_name": "Tumor and model samples with mutations", + "case_list_description": "All tumor and model samples with mutation data", + "case_list_category": "all_cases_with_mutation_data" + }, + "database_pulls": { + "_comment": "This section is used to numerate relevant database schema and tables needed for clinical data and supporting genomic etl files", + "manifests": { + "chdm_phs002301_2021": { + "table": "bix_genomics_file.sd_q8d06qqh-genomics_file_manifest", + "file_type": ["annotated_public_outputs","ctrlfreec_pval","ctrlfreec_info","ctrlfreec_bam_seg"], + "out_file": "chdm_phs002301_2021_genomics_file_manifest.txt" + } + }, + "sample_head": { + "table": "template_sample_header.txt" + }, + "sample_file": { + "table": "brownm28_dev_schema_cbio.chdm_phs002301_2021_data_clinical_sample", + "out_file": "data_clinical_sample.txt" + }, + "patient_head": { + "table": "template_patient_header.txt" + }, + "patient_file": { + "table": "brownm28_dev_schema_cbio.chdm_phs002301_2021_data_clinical_patient", + "out_file": "data_clinical_patient.txt" + }, + "genomics_etl": { + "table": "brownm28_dev_schema_cbio.chdm_phs002301_2021_genomics_etl_file", + "out_file": "cbio_file_name_id.txt" + } + } +} \ No newline at end of file From c4db1574bc681516772f6b8f3354d1e0a566fccf Mon Sep 17 00:00:00 2001 From: Miguel Brown Date: Wed, 10 Jan 2024 09:32:25 -0500 Subject: [PATCH 2/2] :hammer: updated mioncoseq to pull from more studies :pencil: corrected a rampant typo --- .../openPBTA/openpbta_case_meta_config.json | 4 ++-- .../openTARGETS/case_openTargets_meta_config.json | 4 ++-- .../openpedcan_v11_case_meta_config.json | 4 ++-- .../openpedcan_v12_case_meta_config.json | 4 ++-- .../case_Ijaz_cole_published_meta_config.json | 4 ++-- .../case_cptac_published_meta_config.json | 4 ++-- .../aml_sd_z6mwd3h0_2018_case_meta_config.json | 4 ++-- STUDY_CONFIGS/case_cptac_meta_config.json | 4 ++-- .../chdm_phs001643_2018_case_meta_config.json | 4 ++-- .../chdm_phs002301_2021_case_meta_config.json | 2 +- .../chdm_sd_7spqtt8m_case_meta_config.json | 4 ++-- STUDY_CONFIGS/oligo_nation_case_meta_config.json | 4 ++-- STUDY_CONFIGS/open_chordoma_case_meta_config.json | 4 ++-- .../os_sd_zxjffmef_2015_case_meta_config.json | 4 ++-- STUDY_CONFIGS/pbta_all_case_meta_config.json | 4 ++-- STUDY_CONFIGS/pbta_all_treatment_meta_config.json | 4 ++-- STUDY_CONFIGS/pbta_mioncoseq_case_meta_config.json | 14 ++++++++++++-- .../tll_sd_aq9kvn5p_2019_case_meta_config.json | 4 ++-- .../x01_nbl_16_maris_case_meta_config.json | 4 ++-- 19 files changed, 47 insertions(+), 37 deletions(-) diff --git a/COLLABORATIONS/openPBTA/openpbta_case_meta_config.json b/COLLABORATIONS/openPBTA/openpbta_case_meta_config.json index 12f9b97..beb0a54 100644 --- 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 index 6f891c6..9606512 100644 --- 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 index 34593f3..c06c560 100644 --- 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 index 2edad36..b79bb73 100644 --- 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 index b02a102..5bd4fd4 100644 --- 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 index 45fece2..265e605 100644 --- 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 index 13bab5c..0d1c751 100644 --- 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 index f514513..58550d7 100644 --- 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 index 69e44e9..d08f011 100644 --- 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 index 4af1cf8..c2c3865 100644 --- 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: Release Notes", - "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 index f0a566a..7b72f71 100644 --- 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 index 1eb9e98..8cbb308 100644 --- 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 index 6c525ec..99f27d9 100644 --- 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 index f84196d..62dc9f8 100644 --- 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 index c79dfc0..35da286 100644 --- 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 index c5847cc..b6b0360 100644 --- 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 index 031a3e3..65a0cd7 100644 --- 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 index 1c0c60f..b2e1c4b 100644 --- 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 index 25dd629..2f3521e 100644 --- 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" },