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Merge pull request #81 from icgc-argo/fix_genome_build
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remove genome_build and genome_annotation from the required fields of…
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@lindaxiang
lindaxiang authored Apr 19, 2024
2 parents b59ceef + c65cb1b commit ce411f6
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Showing 10 changed files with 229 additions and 37 deletions.
4 changes: 2 additions & 2 deletions example_payloads/rna-seq/qc_metrics.rna_aln.json
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"inputs": [
{
"analysis_type": "sequencing_experiment",
"input_analysis_id": null
"input_analysis_id": "0048d713-2088-4c54-88d7-1320885c5477"
}
]
},
Expand Down Expand Up @@ -127,7 +127,7 @@
"experimental_strategy": "RNA-Seq",
"sequencing_date": "2021-04-21",
"library_isolation_protocol": "",
"library_prepation_kit": "",
"library_preparation_kit": "",
"library_strandedness": "FIRST_READ_SENSE_STRAND",
"rin": 9,
"dv200": "90%",
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2 changes: 1 addition & 1 deletion example_payloads/rna-seq/sequencing_alignment.json
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Expand Up @@ -62,7 +62,7 @@
"library_preparation_kit": "TruSeq",
"library_strandedness": "UNSTRANDED",
"rin": 9.0,
"dv200": 0.7,
"dv200": "70%",
"spike_ins_included": true,
"spike_ins_fasta": "",
"spike_ins_concentration": "",
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4 changes: 2 additions & 2 deletions example_payloads/rna-seq/splice_junctions.json
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Expand Up @@ -13,7 +13,7 @@
"inputs": [
{
"analysis_type": "sequencing_experiment",
"input_analysis_id": null
"input_analysis_id": "0048d713-2088-4c54-88d7-1320885c5477"
}
]
},
Expand Down Expand Up @@ -60,7 +60,7 @@
"experimental_strategy": "RNA-Seq",
"sequencing_date": "2021-04-21",
"library_isolation_protocol": "",
"library_prepation_kit": "",
"library_preparation_kit": "",
"library_strandedness": "FIRST_READ_ANTISENSE_STRAND",
"rin": 9,
"dv200": "90%",
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4 changes: 2 additions & 2 deletions example_payloads/rna-seq/supplement.json
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Expand Up @@ -13,7 +13,7 @@
"inputs": [
{
"analysis_type": "sequencing_experiment",
"input_analysis_id": null
"input_analysis_id": "0048d713-2088-4c54-88d7-1320885c5477"
}
]
},
Expand Down Expand Up @@ -66,7 +66,7 @@
"experimental_strategy": "RNA-Seq",
"sequencing_date": "2021-04-21",
"library_isolation_protocol": "",
"library_prepation_kit": "",
"library_preparation_kit": "",
"library_strandedness": "FIRST_READ_SENSE_STRAND",
"rin": 9,
"dv200": "90%",
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42 changes: 37 additions & 5 deletions schemas/qc_metrics.json
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Expand Up @@ -293,8 +293,7 @@
},
"required": [
"workflow_name",
"workflow_version",
"genome_build"
"workflow_version"
],
"properties": {
"workflow_name": {
Expand Down Expand Up @@ -367,9 +366,8 @@
"if": {
"properties": {
"workflow_name": {
"enum": [
"RNA Seq Alignment"
]
"type": "string",
"pattern": "^.*RNA-Seq.*$"
}
}
},
Expand All @@ -384,6 +382,40 @@
"genome_annotation"
]
}
},
{
"if": {
"properties": {
"workflow_name": {
"enum": [
"Pre Alignment QC"
]
}
}
},
"then": {
"properties": {
"genome_build": {
"type": "string"
}
}
},
"else": {
"properties": {
"genome_build": {
"type": "string",
"enum": [
"GRCh38_hla_decoy_ebv",
"GRCh38_Verily_v1",
"GRCh38",
"GRCh37"
]
}
},
"required": [
"genome_build"
]
}
}
]
}
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42 changes: 37 additions & 5 deletions schemas/sequencing_alignment.json
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Expand Up @@ -437,8 +437,7 @@
},
"required": [
"workflow_name",
"workflow_version",
"genome_build"
"workflow_version"
],
"properties": {
"workflow_name": {
Expand Down Expand Up @@ -511,9 +510,8 @@
"if": {
"properties": {
"workflow_name": {
"enum": [
"RNA Seq Alignment"
]
"type": "string",
"pattern": "^.*RNA-Seq.*$"
}
}
},
Expand All @@ -528,6 +526,40 @@
"genome_annotation"
]
}
},
{
"if": {
"properties": {
"workflow_name": {
"enum": [
"Pre Alignment QC"
]
}
}
},
"then": {
"properties": {
"genome_build": {
"type": "string"
}
}
},
"else": {
"properties": {
"genome_build": {
"type": "string",
"enum": [
"GRCh38_hla_decoy_ebv",
"GRCh38_Verily_v1",
"GRCh38",
"GRCh37"
]
}
},
"required": [
"genome_build"
]
}
}
]
}
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42 changes: 37 additions & 5 deletions schemas/splice_junctions.json
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Expand Up @@ -293,8 +293,7 @@
},
"required": [
"workflow_name",
"workflow_version",
"genome_build"
"workflow_version"
],
"properties": {
"workflow_name": {
Expand Down Expand Up @@ -367,9 +366,8 @@
"if": {
"properties": {
"workflow_name": {
"enum": [
"RNA Seq Alignment"
]
"type": "string",
"pattern": "^.*RNA-Seq.*$"
}
}
},
Expand All @@ -384,6 +382,40 @@
"genome_annotation"
]
}
},
{
"if": {
"properties": {
"workflow_name": {
"enum": [
"Pre Alignment QC"
]
}
}
},
"then": {
"properties": {
"genome_build": {
"type": "string"
}
}
},
"else": {
"properties": {
"genome_build": {
"type": "string",
"enum": [
"GRCh38_hla_decoy_ebv",
"GRCh38_Verily_v1",
"GRCh38",
"GRCh37"
]
}
},
"required": [
"genome_build"
]
}
}
]
}
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42 changes: 37 additions & 5 deletions schemas/supplement.json
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Expand Up @@ -293,8 +293,7 @@
},
"required": [
"workflow_name",
"workflow_version",
"genome_build"
"workflow_version"
],
"properties": {
"workflow_name": {
Expand Down Expand Up @@ -367,9 +366,8 @@
"if": {
"properties": {
"workflow_name": {
"enum": [
"RNA Seq Alignment"
]
"type": "string",
"pattern": "^.*RNA-Seq.*$"
}
}
},
Expand All @@ -384,6 +382,40 @@
"genome_annotation"
]
}
},
{
"if": {
"properties": {
"workflow_name": {
"enum": [
"Pre Alignment QC"
]
}
}
},
"then": {
"properties": {
"genome_build": {
"type": "string"
}
}
},
"else": {
"properties": {
"genome_build": {
"type": "string",
"enum": [
"GRCh38_hla_decoy_ebv",
"GRCh38_Verily_v1",
"GRCh38",
"GRCh37"
]
}
},
"required": [
"genome_build"
]
}
}
]
}
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42 changes: 37 additions & 5 deletions schemas/variant_calling.json
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Expand Up @@ -294,8 +294,7 @@
},
"required": [
"workflow_name",
"workflow_version",
"genome_build"
"workflow_version"
],
"properties": {
"workflow_name": {
Expand Down Expand Up @@ -368,9 +367,8 @@
"if": {
"properties": {
"workflow_name": {
"enum": [
"RNA Seq Alignment"
]
"type": "string",
"pattern": "^.*RNA-Seq.*$"
}
}
},
Expand All @@ -385,6 +383,40 @@
"genome_annotation"
]
}
},
{
"if": {
"properties": {
"workflow_name": {
"enum": [
"Pre Alignment QC"
]
}
}
},
"then": {
"properties": {
"genome_build": {
"type": "string"
}
}
},
"else": {
"properties": {
"genome_build": {
"type": "string",
"enum": [
"GRCh38_hla_decoy_ebv",
"GRCh38_Verily_v1",
"GRCh38",
"GRCh37"
]
}
},
"required": [
"genome_build"
]
}
}
]
},
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