@hms-dbmi-bgm/react-workflow-viz
Version:
React component for visualizing CWL-like workflows and provenance graphs.
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JSON
[
{
"name":"/workflow-runs-awsem/5c7c29ea-5ce1-42fc-a09d-a8f9f80626b4/",
"meta":{
"display_title":"workflow_bwa-mem_no_unzip-check v8 run 2019-08-08 01:03:06.639362",
"status":"in review",
"run_status":"complete",
"@type":[
"WorkflowRunAwsem",
"WorkflowRun",
"Item"
],
"@id":"/workflow-runs-awsem/5c7c29ea-5ce1-42fc-a09d-a8f9f80626b4/",
"date_created":"2019-08-27T04:03:40.660199+00:00",
"analysis_step_types":[
"processing"
],
"workflow":{
"@id":"/workflows/9e094699-561b-4396-8d6a-ffc45f98c5e1/",
"@type":[
"Workflow",
"Item"
],
"display_title":"Paired-end reads alignment to reference plus output integrity-check - GAPWF9HYUJB9",
"accession":"GAPWF9HYUJB9",
"steps":[
{
"meta":{
"software_used":[
"42adeb1b-c46c-4ba8-b191-56036ddcd544"
],
"analysis_step_types":[
"Align paired-end reads to reference genome"
]
},
"name":"bwa-mem",
"inputs":[
{
"meta":{
"type":"data file",
"global":true,
"cardinality":"single",
"file_format":"c13d06cf-218e-4f61-aaf0-91f226248b2c"
},
"name":"fastq_R1",
"source":[
{
"name":"fastq_R1"
}
]
},
{
"meta":{
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"global":true,
"cardinality":"single",
"file_format":"c13d06cf-218e-4f61-aaf0-91f226248b2c"
},
"name":"fastq_R2",
"source":[
{
"name":"fastq_R2"
}
]
},
{
"meta":{
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"file_format":"813b0001-5f3f-4e28-9203-4cdf261e19c4"
},
"name":"reference",
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{
"name":"reference"
}
]
},
{
"meta":{
"type":"parameter",
"global":true,
"cardinality":"single"
},
"name":"nthreads",
"source":[
{
"name":"nthreads"
}
]
}
],
"outputs":[
{
"meta":{
"type":"data file",
"global":true,
"cardinality":"single",
"file_format":"bam"
},
"name":"raw_bam",
"target":[
{
"name":"raw_bam",
"step":"integrity-check"
}
]
}
]
},
{
"meta":{
"software_used":[
"3f2d3b0e-0365-4212-9468-c16ad9531c4d"
],
"analysis_step_types":[
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]
},
"name":"integrity-check",
"inputs":[
{
"meta":{
"type":"data file",
"global":false,
"cardinality":"single",
"file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
},
"name":"raw_bam",
"source":[
{
"name":"raw_bam",
"step":"bwa-mem"
}
]
},
{
"meta":{
"type":"parameter",
"global":true,
"cardinality":"single"
},
"name":"count",
"source":[
{
"name":"count"
}
]
}
],
"outputs":[
{
"meta":{
"type":"QC",
"global":true,
"cardinality":"single"
},
"name":"raw_bam-check",
"target":[
{
"name":"raw_bam-check"
}
]
}
]
}
],
"uuid":"9e094699-561b-4396-8d6a-ffc45f98c5e1",
"category":[
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}
},
"inputs":[
{
"name":"fastq_R1",
"source":[
{
"name":"fastq_R1",
"for_file":"/files-fastq/GAPFIT9HIA1D/"
}
],
"meta":{
"in_path":true,
"global":true,
"type":"data file"
},
"run_data":{
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{
"@id":"/files-fastq/GAPFIT9HIA1D/",
"uuid":"376ee6fc-7236-404b-90da-62e835119eb4",
"display_title":"GAPFIT9HIA1D.fastq.gz",
"accession":"GAPFIT9HIA1D",
"@type":[
"FileFastq",
"File",
"Item"
],
"quality_metric":{
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"@type":[
"QualityMetricFastqc",
"QualityMetric",
"Item"
],
"display_title":"QualityMetricFastqc from 2019-08-27",
"Sequence length":"35-150",
"Total Sequences":516716922,
"url":"https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIYT4W47L/fastqc_report.html",
"overall_quality_status":"PASS",
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"href":"/files-fastq/GAPFIT9HIA1D/@@download/GAPFIT9HIA1D.fastq.gz",
"filename":"888968-UDN193590-P_R1.fastq.gz",
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"@type":[
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}
},
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"status":"uploaded"
}
],
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"meta":[
{
"ordinal":1,
"dimension":"0",
"workflow_argument_name":"fastq_R1"
}
]
}
},
{
"name":"fastq_R2",
"source":[
{
"name":"fastq_R2",
"for_file":"/files-fastq/GAPFIN16EGPT/"
}
],
"meta":{
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"accession":"GAPFIN16EGPT",
"@type":[
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],
"quality_metric":{
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"display_title":"QualityMetricFastqc from 2019-08-27",
"Sequence length":"35-150",
"@id":"/quality-metrics-fastqc/c6f754d0-1ff1-4f4f-a3d5-e5029382474f/",
"uuid":"c6f754d0-1ff1-4f4f-a3d5-e5029382474f",
"@type":[
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],
"url":"https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIYOB1C8Y/fastqc_report.html",
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"href":"/files-fastq/GAPFIN16EGPT/@@download/GAPFIN16EGPT.fastq.gz",
"filename":"888968-UDN193590-P_R2.fastq.gz",
"file_format":{
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}
},
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"status":"uploaded"
}
],
"type":"input",
"meta":[
{
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"dimension":"0",
"workflow_argument_name":"fastq_R2"
}
]
}
},
{
"name":"reference",
"source":[
{
"name":"reference",
"for_file":"/files-reference/GAPFI4U1HXIY/"
}
],
"meta":{
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"global":true,
"type":"reference file"
},
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{
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"uuid":"b24ed5ed-a037-48a0-a938-3fecfb90d0cf",
"display_title":"GAPFI4U1HXIY.bwt",
"accession":"GAPFI4U1HXIY",
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"Item"
],
"href":"/files-reference/GAPFI4U1HXIY/@@download/GAPFI4U1HXIY.bwt",
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"display_title":"bwt",
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],
"type":"input",
"meta":[
{
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"workflow_argument_name":"reference"
}
]
}
}
],
"outputs":[
{
"name":"raw_bam",
"target":[
{
"name":"raw_bam"
},
{
"name":"input_bam",
"step":"/workflow-runs-awsem/935b7578-8d4e-4530-85fa-c7a305f92263/",
"for_file":"/files-processed/GAPFITKM4JXJ/"
}
],
"meta":{
"type":"data file",
"global":true,
"in_path":true
},
"run_data":{
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{
"@id":"/files-processed/GAPFITKM4JXJ/",
"uuid":"6d44733a-d8b1-485a-bf1a-f0db43e8b167",
"display_title":"GAPFITKM4JXJ.bam",
"accession":"GAPFITKM4JXJ",
"@type":[
"FileProcessed",
"File",
"Item"
],
"quality_metric":{
"display_title":"QualityMetricBamcheck from 2019-08-27",
"@id":"/quality-metrics-bamcheck/b11f7ad5-aadc-4a2a-a5ae-de18214f1b61/",
"uuid":"b11f7ad5-aadc-4a2a-a5ae-de18214f1b61",
"@type":[
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"Item"
],
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}
},
"href":"/files-processed/GAPFITKM4JXJ/@@download/GAPFITKM4JXJ.bam",
"file_format":{
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"file_format":"bam",
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}
},
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"status":"uploaded"
}
],
"type":"input",
"meta":[
{
"type":"Output processed file",
"format":"/file-formats/bam/",
"upload_key":"6d44733a-d8b1-485a-bf1a-f0db43e8b167/4DNFIWMJ1U2F.bam"
}
]
}
}
]
},
{
"name":"/workflow-runs-awsem/935b7578-8d4e-4530-85fa-c7a305f92263/",
"meta":{
"display_title":"workflow_readgroups-check v9 run 2019-08-08 22:02:45.321937",
"status":"in review",
"run_status":"complete",
"@type":[
"WorkflowRunAwsem",
"WorkflowRun",
"Item"
],
"@id":"/workflow-runs-awsem/935b7578-8d4e-4530-85fa-c7a305f92263/",
"date_created":"2019-08-27T04:03:53.637995+00:00",
"analysis_step_types":[
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],
"workflow":{
"@id":"/workflows/548e63a4-1936-4f68-8e8d-8e4658767911/",
"@type":[
"Workflow",
"Item"
],
"display_title":"Add read groups plus output integrity-check - GAPWFECVBVP9",
"accession":"GAPWFECVBVP9",
"steps":[
{
"meta":{
"software_used":[
"d7ac4c75-e133-4a8e-a19e-b7e87873cc16"
],
"analysis_step_types":[
"Add read groups to bam input file"
]
},
"name":"add-readgroups",
"inputs":[
{
"meta":{
"type":"data file",
"global":true,
"cardinality":"single",
"file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
},
"name":"input_bam",
"source":[
{
"name":"input_bam"
}
]
},
{
"meta":{
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"global":true,
"cardinality":"single"
},
"name":"sample_name",
"source":[
{
"name":"sample_name"
}
]
},
{
"meta":{
"type":"parameter",
"global":true,
"cardinality":"single"
},
"name":"nthreads",
"source":[
{
"name":"nthreads"
}
]
}
],
"outputs":[
{
"meta":{
"type":"data file",
"global":true,
"cardinality":"single",
"file_format":"bam"
},
"name":"bam_w_readgroups",
"target":[
{
"name":"bam_w_readgroups",
"step":"integrity-check"
}
]
}
]
},
{
"meta":{
"software_used":[
"3f2d3b0e-0365-4212-9468-c16ad9531c4d"
],
"analysis_step_types":[
"Check integrity of output file"
]
},
"name":"integrity-check",
"inputs":[
{
"meta":{
"type":"data file",
"global":false,
"cardinality":"single",
"file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
},
"name":"bam_w_readgroups",
"source":[
{
"name":"bam_w_readgroups",
"step":"add-readgroups"
}
]
},
{
"meta":{
"type":"parameter",
"global":true,
"cardinality":"single"
},
"name":"count",
"source":[
{
"name":"count"
}
]
}
],
"outputs":[
{
"meta":{
"type":"QC",
"global":true,
"cardinality":"single"
},
"name":"bam_w_readgroups-check",
"target":[
{
"name":"bam_w_readgroups-check"
}
]
}
]
}
],
"uuid":"548e63a4-1936-4f68-8e8d-8e4658767911",
"category":[
"processing"
],
"experiment_types":[
]
}
},
"inputs":[
{
"name":"input_bam",
"source":[
{
"name":"raw_bam",
"step":"/workflow-runs-awsem/5c7c29ea-5ce1-42fc-a09d-a8f9f80626b4/",
"for_file":"/files-processed/GAPFITKM4JXJ/",
"workflow":"/workflows/9e094699-561b-4396-8d6a-ffc45f98c5e1/"
}
],
"meta":{
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"global":true,
"type":"data file"
},
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{
"@id":"/files-processed/GAPFITKM4JXJ/",
"uuid":"6d44733a-d8b1-485a-bf1a-f0db43e8b167",
"display_title":"GAPFITKM4JXJ.bam",
"accession":"GAPFITKM4JXJ",
"@type":[
"FileProcessed",
"File",
"Item"
],
"quality_metric":{
"display_title":"QualityMetricBamcheck from 2019-08-27",
"@id":"/quality-metrics-bamcheck/b11f7ad5-aadc-4a2a-a5ae-de18214f1b61/",
"uuid":"b11f7ad5-aadc-4a2a-a5ae-de18214f1b61",
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],
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"href":"/files-processed/GAPFITKM4JXJ/@@download/GAPFITKM4JXJ.bam",
"file_format":{
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],
"type":"input",
"meta":[
{
"ordinal":1,
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"workflow_argument_name":"input_bam"
}
]
}
}
],
"outputs":[
{
"name":"bam_w_readgroups",
"target":[
{
"name":"bam_w_readgroups"
},
{
"name":"input_bams",
"step":"/workflow-runs-awsem/5717940c-2550-48b6-a16b-99517e95fc9c/",
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}
],
"meta":{
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},
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},
"href":"/files-processed/GAPFIJ7FULOF/@@download/GAPFIJ7FULOF.bam",
"description":"Intermediate alingnemnt file",
"file_format":{
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