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sample_single_donor.json
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{
"project" : "BRCA-UK",
"donor_attributes" : {
"example_donor_attribute:" : "string"
},
"tumour_specimen" : [
{
"alignment" : {
"sequencing_strategy" : "WGS",
"workflows" : [
{
"host_metrics" : {
"vm_instance_cores" : 4,
"vm_region" : "us-east-1",
"vm_instance_mem_gb" : 256,
"vm_instance_type" : "m1.xlarge",
"vm_location" : "aws"
},
"workflow_bundle_url" : "http://foo.bar/bwa-workflow",
"workflow_description" : "This is the alignment for specimen PD41189 from donor CGP_donor_1199138.",
"workflow_outputs" : {
"foo.bam" : {
"file_type_cv_terms" : [
"EDAM:1293829"
],
"file_type_label" : "bam"
},
"foo.bam.bai" : {
"file_type_cv_terms" : [
"EDAM:278392"
],
"file_type_label" : "bai"
}
},
"workflow_version" : "1.0.0",
"timing_metrics" : {
"overall_start_time_utc" : "Thu Apr 14 22:18:30 UTC 2016",
"step_timing" : {
"alignment" : {
"start_time_utc" : "Thu Apr 14 22:18:30 UTC 2016",
"stop_time_utc" : "Thu Apr 14 24:18:30 UTC 2016",
"walltime_seconds" : 60000
}
},
"overall_stop_time_utc" : "Thu Apr 14 24:18:30 UTC 2016",
"overall_walltime_seconds" : 60000
},
"workflow_name" : "bwa-mem-alignment",
"workflow_params" : {
"param1" : 12121,
"param2" : 2389239
},
"workflow_source_url" : "http://foo.bar/bwa-workflow-src",
"workflow_inputs" : [
{
"file_storage_bundle_files" : {
"file_storage_metadata_json_uri" : "153c380c-0bcb-4ee9-abdf-629db73a62e5",
"foo1.fastq.gz" : {
"file_type_cv_terms" : [
"EDAM:123232"
],
"file_storage_uri" : "ae616ade-3734-4c48-a609-f2b292ecdbc7",
"file_type_label" : "fastq"
},
"file_storage_bundle_uri" : "0e99945c-631e-4123-9158-5132a8fe2150",
"foo2.fastq.gz" : {
"file_type_cv_terms" : [
"EDAM:123232"
],
"file_type_label" : "fastq",
"file_storage_uri" : "9014505b-fa59-4913-a05c-4666c6efe198"
}
}
}
],
"qc_metrics" : {
"coverage_average" : 123.4,
"insert_size_average" : 10456,
"insert_size_sd" : 313
}
}
]
},
"submitter_specimen_type" : "Primary tumour - solid tissue",
"analysis_specimen_attributes" : [
{
"example_specimen_attribute:" : "string"
}
],
"sequencing_upload" : {
"workflows" : [
{
"workflow_description" : "This is the upload of the fastq from a sample using the submission script.",
"workflow_bundle_url" : "http://foo.bar/tool",
"host_metrics" : {
"vm_instance_mem_gb" : 256,
"vm_instance_type" : "m1.xlarge",
"vm_location" : "aws",
"vm_instance_cores" : 4,
"vm_region" : "us-east-1"
},
"workflow_inputs" : {},
"qc_metrics" : {},
"workflow_source_url" : "http://foo.bar/tool-src",
"workflow_name" : "fastq-submission",
"workflow_version" : "1.0.0",
"timing_metrics" : {},
"workflow_outputs" : {
"foo1.fastq.gz" : {
"file_type_label" : "fastq",
"file_type_cv_terms" : [
"EDAM:123232"
]
},
"foo2.fastq.gz" : {
"file_type_label" : "fastq",
"file_type_cv_terms" : [
"EDAM:123232"
]
}
}
}
]
},
"tumour_sample_attributes" : [
{
"submitter_sample_id" : "PD41189-1",
"analysis_sample_attributes" : [
{
"example_sample_attribute" : "EGAN00001000597"
}
]
}
],
"submitter_specimen_id" : "PD41189"
}
],
"somatic_variant_calling" : {
"workflows" : [
{
"workflow_inputs" : [
{
"file_storage_bundle_files" : {
"foo.bam" : {
"file_type_label" : "bam",
"file_storage_uri" : "ae616ade-3734-4c48-a609-f2b292ecdbc7",
"file_type_cv_terms" : [
"EDAM:1293829"
]
},
"foo.bam.bai" : {
"file_storage_uri" : "04731ba6-9d5a-42f8-a25a-bf6416d7f00a",
"file_type_label" : "bai",
"file_type_cv_terms" : [
"EDAM:123232"
]
}
},
"file_storage_bundle_uri" : "b6525378-d904-4276-b42a-5cf01506ca8a",
"file_storage_metadata_json_uri" : "050a0b5b-ba9a-4200-96f8-fc7982f02416"
}
],
"qc_metrics" : {
"variants_called" : 3456423,
"contamination_percent" : 1.2
},
"workflow_outputs" : [
{
"foo.vcf" : {
"file_type_label" : "vcf",
"file_type_cv_terms" : [
"EDAM:12293829"
]
},
"foo.vcf.tbi" : {
"file_type_label" : "tbi",
"file_type_cv_terms" : [
"EDAM:2783392"
]
}
}
],
"workflow_version" : "1.0.0",
"timing_metrics" : {
"overall_start_time_utc" : "Thu Apr 14 22:18:30 UTC 2016",
"step_timing" : {
"variant_calling" : {
"start_time_utc" : "Thu Apr 14 22:18:30 UTC 2016",
"stop_time_utc" : "Thu Apr 14 24:18:30 UTC 2016",
"walltime_seconds" : 60000
}
},
"overall_walltime_seconds" : 60000,
"overall_stop_time_utc" : "Thu Apr 14 24:18:30 UTC 2016"
},
"workflow_name" : "sanger-variant-calling",
"workflow_source_url" : "http://foo.bar/sanger-workflow-src",
"workflow_params" : {
"param2" : 2389239,
"param1" : 12121
},
"analysis_attributes" : {
"use_ctrl" : "PD41189",
"assembly_short_name" : "GRCh37"
},
"workflow_bundle_url" : "http://foo.bar/sanger-workflow",
"workflow_description" : "This is the variant calling for specimen PD41189 from donor CGP_donor_1199138.",
"host_metrics" : {
"vm_instance_mem_gb" : 256,
"vm_instance_type" : "m1.xlarge",
"vm_location" : "aws",
"vm_instance_cores" : 4,
"vm_region" : "us-east-1"
}
}
],
"variant_calling_strategy" : "string"
},
"normal_specimen" : [
{
"submitter_specimen_type" : "Normal - solid tissue",
"specimen_attributes" :
{
"example_specimen_attribute:" : "string"
}
,
"normal_sample_attributes" : [
{
"submitter_sample_id" : "PD41189-1",
"analysis_sample_attributes" : [
{
"example_sample_attribute" : "EGAN00001000597"
}
]
}
],
"alignment" : {
"sequencing_strategy" : "WGS",
"workflows" : [
{
"host_metrics" : {
"vm_location" : "aws",
"vm_instance_type" : "m1.xlarge",
"vm_instance_mem_gb" : 256,
"vm_region" : "us-east-1",
"vm_instance_cores" : 4
},
"workflow_description" : "This is the alignment for specimen PD41189 from donor CGP_donor_1199138.",
"workflow_bundle_url" : "http://foo.bar/bwa-workflow",
"workflow_params" : {
"param1" : 12121,
"param2" : 2389239
},
"workflow_source_url" : "http://foo.bar/bwa-workflow-src",
"workflow_name" : "bwa-mem-alignment",
"workflow_version" : "1.0.0",
"timing_metrics" : {
"overall_start_time_utc" : "Thu Apr 14 22:18:30 UTC 2016",
"overall_walltime_seconds" : 60000,
"overall_stop_time_utc" : "Thu Apr 14 24:18:30 UTC 2016",
"step_timing" : {
"alignment" : {
"stop_time_utc" : "Thu Apr 14 24:18:30 UTC 2016",
"walltime_seconds" : 60000,
"start_time_utc" : "Thu Apr 14 22:18:30 UTC 2016"
}
}
},
"workflow_outputs" : {
"foo.bam.bai" : {
"file_type_label" : "bai",
"file_type_cv_terms" : [
"EDAM:278392"
]
},
"foo.bam" : {
"file_type_label" : "bam",
"file_type_cv_terms" : [
"EDAM:1293829"
]
}
},
"qc_metrics" : {
"insert_size_average" : 10456,
"insert_size_sd" : 313,
"coverage_average" : 123.4
},
"workflow_inputs" : [
{
"file_storage_bundle_files" : {
"file_storage_metadata_json_uri" : "153c380c-0bcb-4ee9-abdf-629db73a62e5",
"foo1.fastq.gz" : {
"file_type_cv_terms" : [
"EDAM:123232"
],
"file_type_label" : "fastq",
"file_storage_uri" : "ae616ade-3734-4c48-a609-f2b292ecdbc7"
},
"foo2.fastq.gz" : {
"file_type_cv_terms" : [
"EDAM:123232"
],
"file_type_label" : "fastq",
"file_storage_uri" : "9014505b-fa59-4913-a05c-4666c6efe198"
},
"file_storage_bundle_uri" : "0e99945c-631e-4123-9158-5132a8fe2150"
}
}
]
}
]
},
"submitter_specimen_id" : "PD41189",
"germline_variant_calling" : {
"workflows" : [
{
"qc_metrics" : {
"variants_called" : 3456423,
"contamination_percent" : 1.2
},
"workflow_inputs" : [
{
"file_storage_metadata_json_uri" : "050a0b5b-ba9a-4200-96f8-fc7982f02416",
"file_storage_bundle_uri" : "b6525378-d904-4276-b42a-5cf01506ca8a",
"file_storage_bundle_files" : {
"foo.bam" : {
"file_storage_uri" : "ae616ade-3734-4c48-a609-f2b292ecdbc7",
"file_type_label" : "bam",
"file_type_cv_terms" : [
"EDAM:1293829"
]
},
"foo.bam.bai" : {
"file_type_label" : "bai",
"file_storage_uri" : "04731ba6-9d5a-42f8-a25a-bf6416d7f00a",
"file_type_cv_terms" : [
"EDAM:123232"
]
}
}
}
],
"workflow_name" : "sanger-variant-calling",
"workflow_source_url" : "http://foo.bar/sanger-workflow-src",
"workflow_params" : {
"param2" : 2389239,
"param1" : 12121
},
"workflow_outputs" : [
{
"foo.vcf.tbi" : {
"file_type_label" : "tbi",
"file_type_cv_terms" : [
"EDAM:2783392"
]
},
"foo.vcf" : {
"file_type_label" : "vcf",
"file_type_cv_terms" : [
"EDAM:12293829"
]
}
}
],
"timing_metrics" : {
"step_timing" : {
"variant_calling" : {
"walltime_seconds" : 60000,
"stop_time_utc" : "Thu Apr 14 24:18:30 UTC 2016",
"start_time_utc" : "Thu Apr 14 22:18:30 UTC 2016"
}
},
"overall_walltime_seconds" : 60000,
"overall_stop_time_utc" : "Thu Apr 14 24:18:30 UTC 2016",
"overall_start_time_utc" : "Thu Apr 14 22:18:30 UTC 2016"
},
"workflow_version" : "1.0.0",
"workflow_description" : "This is the variant calling for specimen PD41189 from donor CGP_donor_1199138.",
"analysis_attributes" : {
"assembly_short_name" : "GRCh37",
"use_ctrl" : "PD41189"
},
"workflow_bundle_url" : "http://foo.bar/sanger-workflow",
"host_metrics" : {
"vm_region" : "us-east-1",
"vm_instance_cores" : 4,
"vm_location" : "aws",
"vm_instance_type" : "m1.xlarge",
"vm_instance_mem_gb" : 256
}
}
]
}
}
],
"submitter_donor_id" : "CGP_donor_1199138",
"program" : "ICGC",
"center_name" : "WTSI"
}