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[GH-1205] TDR schemas for sarscov2_illumina_full pipeline #328

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merged 11 commits into from
Feb 22, 2021
Merged

[GH-1205] TDR schemas for sarscov2_illumina_full pipeline #328

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7256b20
add augur-from-assemblies outputs dataset definition
ehigham Feb 18, 2021
918487d
add augur-from-assemblies womtool description
ehigham Feb 18, 2021
c9328d7
locate dataset definition relative to `test/resources/datasets/`
ehigham Feb 18, 2021
845da76
bump description to v2.1.12.0 as v2.1.8.0 is broken
ehigham Feb 19, 2021
27cc7ff
remove unnecessary `->>`
ehigham Feb 22, 2021
86713d6
format consistently
ehigham Feb 22, 2021
3d03756
repurpose `augur_from_assembles` schema for `sarscov2_illumina_full`
ehigham Feb 22, 2021
11f8c9f
fix schema
ehigham Feb 22, 2021
01c5618
add inputs schema
ehigham Feb 22, 2021
88745e1
repurpose `augur_from_assembles` description for `sarscov2_illumina_f…
ehigham Feb 22, 2021
45aed05
set primaryKeys to the non-optional pipeline inputs
ehigham Feb 22, 2021
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66 changes: 66 additions & 0 deletions api/test/resources/datasets/sarscov2-illumina-full-inputs.json
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Original file line number Diff line number Diff line change
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{
"name": "sarscov2_illumina_full_inputs",
"description": "COVID-19 sarscov2_illumina_full pipeline inputs",
"defaultProfileId": "390e7a85-d47f-4531-b612-165fc977d3bd",
"schema": {
"tables": [
{
"name": "sarscov2_illumina_full_inputs",
"columns": [
{
"name": "flowcell_tgz",
"datatype": "fileref"
},
{
"name": "reference_fasta",
"datatype": "fileref"
},
{
"name": "amplicon_bed_prefix",
"datatype": "string"
},
{
"name": "biosample_attributes",
"datatype": "fileref",
"array_of": true
},
{
"name": "instrument_model",
"datatype": "string"
},
{
"name": "sra_title",
"datatype": "string"
},
{
"name": "min_genome_bases",
"datatype": "int64"
},
{
"name": "max_vadr_alerts",
"datatype": "int64"
},
{
"name": "workspace_name",
"datatype": "string"
},
{
"name": "terra_project",
"datatype": "string"
}
],
"primaryKey": [
"flowcell_tgz",
"reference_fasta",
"amplicon_bed_prefix",
"instrument_model",
"sra_title"
],
"partitionMode": "date",
"datePartitionOptions": {
"column": "datarepo_ingest_date"
}
}
]
}
}
214 changes: 214 additions & 0 deletions api/test/resources/datasets/sarscov2-illumina-full-outputs.json
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Original file line number Diff line number Diff line change
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{
"name": "sarscov2_illumina_full_outputs",
"description": "COVID-19 sarscov2_illumina_full pipeline outputs",
"defaultProfileId": "390e7a85-d47f-4531-b612-165fc977d3bd",
"schema": {
"tables": [
{
"name": "sarscov2_illumina_full_outputs",
"columns": [
{
"name": "raw_reads_unaligned_bams",
"datatype": "fileref",
"array_of": true
},
{
"name": "cleaned_reads_unaligned_bams",
"datatype": "fileref",
"array_of": true
},
{
"name": "cleaned_bams_tiny",
"datatype": "fileref",
"array_of": true
},
{
"name": "meta_by_filename_json",
"datatype": "fileref"
},
{
"name": "read_counts_raw",
"datatype": "int64",
"array_of": true
},
{
"name": "read_counts_depleted",
"datatype": "int64",
"array_of": true
},
{
"name": "sra_metadata",
"datatype": "fileref"
},
{
"name": "cleaned_bam_uris",
"datatype": "fileref"
},
{
"name": "assemblies_fasta",
"datatype": "fileref",
"array_of": true
},
{
"name": "passing_assemblies_fasta",
"datatype": "fileref",
"array_of": true
},
{
"name": "submittable_assemblies_fasta",
"datatype": "fileref",
"array_of": true
},
{
"name": "max_ntc_bases",
"datatype": "int64"
},
{
"name": "demux_metrics",
"datatype": "fileref",
"array_of": true
},
{
"name": "demux_commonBarcodes",
"datatype": "fileref",
"array_of": true
},
{
"name": "demux_outlierBarcodes",
"datatype": "fileref",
"array_of": true
},
{
"name": "multiqc_report_raw",
"datatype": "fileref"
},
{
"name": "multiqc_report_cleaned",
"datatype": "fileref"
},
{
"name": "spikein_counts",
"datatype": "fileref"
},
{
"name": "assembly_stats_tsv",
"datatype": "fileref"
},
{
"name": "submission_zip",
"datatype": "fileref"
},
{
"name": "submission_xml",
"datatype": "fileref"
},
{
"name": "submit_ready",
"datatype": "fileref"
},
{
"name": "vadr_outputs",
"datatype": "fileref",
"array_of": true
},
{
"name": "genbank_source_table",
"datatype": "fileref"
},
{
"name": "gisaid_fasta",
"datatype": "fileref"
},
{
"name": "gisaid_meta_tsv",
"datatype": "fileref"
},
{
"name": "genbank_fasta",
"datatype": "fileref"
},
{
"name": "nextmeta_tsv",
"datatype": "fileref"
},
{
"name": "assembled_ids",
"datatype": "string",
"array_of": true
},
{
"name": "submittable_ids",
"datatype": "string",
"array_of": true
},
{
"name": "failed_assembly_ids",
"datatype": "string",
"array_of": true
},
{
"name": "failed_annotation_ids",
"datatype": "string",
"array_of": true
},
{
"name": "num_read_files",
"datatype": "int64"
},
{
"name": "num_assembled",
"datatype": "int64"
},
{
"name": "num_failed_assembly",
"datatype": "int64"
},
{
"name": "num_submittable",
"datatype": "int64"
},
{
"name": "num_failed_annotation",
"datatype": "int64"
},
{
"name": "num_samples",
"datatype": "int64"
},
{
"name": "data_table_status",
"datatype": "string"
}
],
"primaryKey": [
"meta_by_filename_json",
"sra_metadata",
"cleaned_bam_uris",
"max_ntc_bases",
"multiqc_report_raw",
"multiqc_report_cleaned",
"spikein_counts",
"assembly_stats_tsv",
"submission_zip",
"submission_xml",
"submit_ready",
"genbank_source_table",
"gisaid_fasta",
"gisaid_meta_tsv",
"genbank_fasta",
"nextmeta_tsv",
"num_read_files",
"num_assembled",
"num_failed_assembly",
"num_submittable",
"num_failed_annotation",
"num_samples"
],
"partitionMode": "date",
"datePartitionOptions": {
"column": "datarepo_ingest_date"
}
}
]
}
}
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