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ruchim/twist_tcap_schema.json

Last active February 10, 2022 16:48
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twist_tcap_schema.json
{
"id": "UUID",
"name": "TwistTCAP_POC_v8",
"description": "Testing things out...",
"defaultProfileId": null,
"dataProject": null,
"defaultSnapshotId": null,
"schema": {
"tables": [
{
"name": "sample",
"columns": [
{
"name": "sample_id",
"datatype": "string",
"array_of": false
},
{
"name": "participant_id",
"datatype": "string",
"array_of": false
},
{
"name": "collaborator_sample_id",
"datatype": "string",
"array_of": false
},
{
"name": "collaborator_participant_id",
"datatype": "string",
"array_of": false
},
{
"name": "root_sample_id",
"datatype": "string",
"array_of": false
},
{
"name": "picard_reads_aligned_in_pairs",
"datatype": "numeric",
"array_of": false
},
{
"name": "fp_lod_expected_sample",
"datatype": "numeric",
"array_of": false
},
{
"name": "transcriptome_bam",
"datatype": "fileref",
"array_of": false
},
{
"name": "transcriptome_bam_index",
"datatype": "fileref",
"array_of": false
},
{
"name": "transcriptome_duplicate_metrics_file",
"datatype": "fileref",
"array_of": false
},
{
"name": "genome_bam",
"datatype": "fileref",
"array_of": false
},
{
"name": "genome_bam_index",
"datatype": "fileref",
"array_of": false
},
{
"name": "picard_duplicate_metrics_file",
"datatype": "fileref",
"array_of": false
},
{
"name": "fastq1",
"datatype": "fileref",
"array_of": false
},
{
"name": "fastq2",
"datatype": "fileref",
"array_of": false
},
{
"name": "read1Structure",
"datatype": "string",
"array_of": false
},
{
"name": "read2Structure",
"datatype": "string",
"array_of": false
},
{
"name": "library_name",
"datatype": "string",
"array_of": false
},
{
"name": "platform",
"datatype": "string",
"array_of": false
},
{
"name": "platform_unit",
"datatype": "string",
"array_of": false
},
{
"name": "read_group_name",
"datatype": "string",
"array_of": false
},
{
"name": "sequencing_center",
"datatype": "string",
"array_of": false
},
{
"name": "reference_build",
"datatype": "string",
"array_of": false
},
{
"name": "sample_lsid",
"datatype": "string",
"array_of": false
},
{
"name": "reported_sex",
"datatype": "string",
"array_of": false
},
{
"name": "data_type",
"datatype": "string",
"array_of": false
},
{
"name": "pdo",
"datatype": "string",
"array_of": false
},
{
"name": "research_project",
"datatype": "string",
"array_of": false
},
{
"name": "sample_type",
"datatype": "string",
"array_of": false
},
{
"name": "product",
"datatype": "string",
"array_of": false
},
{
"name": "original_material_type",
"datatype": "string",
"array_of": false
},
{
"name": "material_type",
"datatype": "string",
"array_of": false
},
{
"name": "version_timestamp",
"datatype": "timestamp",
"array_of": false
},
{
"name": "receipt_date",
"datatype": "timestamp",
"array_of": false
},
{
"name": "rnaseqc2_gene_tpm_file",
"datatype": "fileref",
"array_of": false
},
{
"name": "rnaseqc2_gene_counts_file",
"datatype": "fileref",
"array_of": false
},
{
"name": "rnaseqc2_exon_counts_file",
"datatype": "fileref",
"array_of": false
},
{
"name": "rnaseqc2_metrics_file",
"datatype": "fileref",
"array_of": false
},
{
"name": "rnaseqc2_fragment_size_histogram_file",
"datatype": "fileref",
"array_of": false
},
{
"name": "picard_rna_metrics_file",
"datatype": "fileref",
"array_of": false
},
{
"name": "picard_alignment_summary_metrics_file",
"datatype": "fileref",
"array_of": false
},
{
"name": "picard_insert_size_metrics_file",
"datatype": "fileref",
"array_of": false
},
{
"name": "picard_insert_size_histogram_file",
"datatype": "fileref",
"array_of": false
},
{
"name": "picard_base_distribution_by_cycle_metrics_file",
"datatype": "fileref",
"array_of": false
},
{
"name": "picard_base_distribution_by_cycle_pdf_file",
"datatype": "fileref",
"array_of": false
},
{
"name": "picard_quality_by_cycle_metrics_file",
"datatype": "fileref",
"array_of": false
},
{
"name": "picard_quality_by_cycle_pdf_file",
"datatype": "fileref",
"array_of": false
},
{
"name": "picard_quality_distribution_metrics_file",
"datatype": "fileref",
"array_of": false
},
{
"name": "picard_quality_distribution_pdf_file",
"datatype": "fileref",
"array_of": false
},
{
"name": "fp_summary_metrics_file",
"datatype": "fileref",
"array_of": false
},
{
"name": "fp_detail_metrics_file",
"datatype": "fileref",
"array_of": false
},
{
"name": "rna_pipeline_submission_id",
"datatype": "string",
"array_of": false
},
{
"name": "rna_pipeline_workflow_id",
"datatype": "string",
"array_of": false
},
{
"name": "rna_pipeline_run_timestamp",
"datatype": "timestamp",
"array_of": false
},
{
"name": "picard_category",
"datatype": "string",
"array_of": false
},
{
"name": "picard_total_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pf_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pct_pf_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pf_noise_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pf_reads_aligned",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pct_pf_reads_aligned",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pf_aligned_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pf_hq_aligned_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pf_hq_aligned_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pf_hq_aligned_q20_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pf_hq_median_mismatches",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pf_mismatch_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pf_hq_error_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pf_indel_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_mean_read_length",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_sd_read_length",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_median_read_length",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_mad_read_length",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_min_read_length",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_max_read_length",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pct_reads_aligned_in_pairs",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pf_reads_improper_pairs",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pct_pf_reads_improper_pairs",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_bad_cycles",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_strand_balance",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pct_chimeras",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pct_adapter",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pct_softclip",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pct_hardclip",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_avg_pos_3prime_softclip_length",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_median_insert_size",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_mode_insert_size",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_median_absolute_deviation",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_min_insert_size",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_max_insert_size",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_mean_insert_size",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_standard_deviation",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_read_pairs",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_pair_orientation",
"datatype": "string",
"array_of": false
},
{
"name": "picard_rna_metrics_pf_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_pf_aligned_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_ribosomal_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_coding_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_utr_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_intronic_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_intergenic_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_ignored_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_correct_strand_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_incorrect_strand_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_num_r1_transcript_strand_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_num_r2_transcript_strand_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_num_unexplained_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_pct_r1_transcript_strand_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_pct_r2_transcript_strand_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_pct_ribosomal_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_pct_coding_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_pct_utr_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_pct_intronic_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_pct_intergenic_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_pct_mrna_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_pct_usable_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_pct_correct_strand_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_median_cv_coverage",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_median_5prime_bias",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_median_3prime_bias",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_rna_metrics_median_5prime_to_3prime_bias",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_library",
"datatype": "string",
"array_of": false
},
{
"name": "picard_unpaired_reads_examined",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_read_pairs_examined",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_secondary_or_supplementary_rds",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_unmapped_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_unpaired_read_duplicates",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_read_pair_duplicates",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_read_pair_optical_duplicates",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_percent_duplication",
"datatype": "numeric",
"array_of": false
},
{
"name": "picard_estimated_library_size",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_sample",
"datatype": "string",
"array_of": false
},
{
"name": "rnaseqc2_mapping_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_unique_rate_of_mapped",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_duplicate_rate_of_mapped",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_duplicate_rate_of_mapped_excluding_globins",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_base_mismatch",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_end_1_mapping_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_end_2_mapping_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_end_1_mismatch_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_end_2_mismatch_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_expression_profiling_efficiency",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_high_quality_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_exonic_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_intronic_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_intergenic_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_intragenic_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_ambiguous_alignment_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_high_quality_exonic_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_high_quality_intronic_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_high_quality_intergenic_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_high_quality_intragenic_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_high_quality_ambiguous_alignment_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_discard_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_rrna_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_end_1_sense_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_end_2_sense_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_avg_splits_per_read",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_alternative_alignments",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_chimeric_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_chimeric_alignment_rate",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_duplicate_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_end_1_antisense",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_end_2_antisense",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_end_1_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_end_2_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_end_1_mapped_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_end_2_mapped_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_end_1_mismatches",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_end_2_mismatches",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_end_1_sense",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_end_2_sense",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_exonic_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_failed_vendor_qc",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_high_quality_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_intergenic_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_intragenic_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_ambiguous_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_intronic_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_low_mapping_quality",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_low_quality_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_mapped_duplicate_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_mapped_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_mapped_unique_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_mismatched_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_non_globin_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_non_globin_duplicate_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_reads_used_for_intron_exon_counts",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_rrna_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_total_bases",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_total_mapped_pairs",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_total_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_unique_mapping_vendor_qc_passed_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_unpaired_reads",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_read_length",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_genes_detected",
"datatype": "numeric",
"array_of": false
},
{
"name": "rnaseqc2_estimated_library_complexity",
"datatype": "numeric",
"array_of": false
},
{
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