UNPKG

@hms-dbmi-bgm/react-workflow-viz

Version:

React component for visualizing CWL-like workflows and provenance graphs.

1,077 lines (1,071 loc) 110 kB
[ { "outputs":[ { "run_data":{ "type":"input", "meta":[ { "extension":".bam", "type":"Output processed file", "format":"bam", "extra_files":null, "upload_key":"ce272100-17f7-42aa-81d1-38c763df9a18/4DNFI5WUPVXK.bam" } ], "file":[ { "file_format":{ "file_format":"bam", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "@type":[ "FileFormat", "Item" ], "@id":"/file-formats/bam/", "display_title":"bam" }, "file_size":380606337, "experiments":[ { "uuid":"b2e1dd76-e8de-48d8-80f5-339c69094aaa", "@id":"/experiments-repliseq/4DNEXN62FHTX/", "experiment_sets":[ { "uuid":"b6b8efc9-07c4-47f0-9f97-8d6a1c5f179c", "@id":"/experiment-set-replicates/4DNESUJC9Y83/" }, { "uuid":"d4aef6dd-f83b-4659-b0f3-88af71357920", "@id":"/experiment-sets/4DNESEJCRVNR/" } ] } ], "href":"/files-processed/4DNFI5WUPVXK/@@download/4DNFI5WUPVXK.bam", "@id":"/files-processed/4DNFI5WUPVXK/", "status":"released", "quality_metric":{ "uuid":"3baa7405-5490-4f43-afeb-5297f98c314c", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "@type":[ "QualityMetricDedupqcRepliseq", "QualityMetric", "Item" ], "display_title":"QualityMetricDedupqcRepliseq from 2018-05-25", "@id":"/quality-metrics-dedupqc-repliseq/3baa7405-5490-4f43-afeb-5297f98c314c/" }, "file_type":"alignment", "accession":"4DNFI5WUPVXK", "uuid":"ce272100-17f7-42aa-81d1-38c763df9a18", "@type":[ "FileProcessed", "File", "Item" ], "description":"This is an output file of the RepliSeq processing pipeline", "experiment_sets":[ ], "display_title":"4DNFI5WUPVXK.bam" } ] }, "target":[ { "name":"filtered_sorted_deduped_bam" } ], "name":"filtered_sorted_deduped_bam", "meta":{ "global":true, "in_path":true, "type":"data file" } }, { "run_data":{ "type":"input", "meta":[ { "type":"Output processed file", "extra_files":[ { "uuid":"7cdb8876-385f-4212-93bf-841178746da0", "file_format":"bg_px2", "accession":"4DNFIN61HEL4", "href":"/7cdb8876-385f-4212-93bf-841178746da0/@@download/4DNFIN61HEL4.bedGraph.gz.px2", "filename":"4DNFIN61HEL4", "status":"to be uploaded by workflow", "upload_key":"7cdb8876-385f-4212-93bf-841178746da0/4DNFIN61HEL4.bedGraph.gz.px2" }, { "uuid":"7cdb8876-385f-4212-93bf-841178746da0", "file_format":"bw", "accession":"4DNFIN61HEL4", "href":"/7cdb8876-385f-4212-93bf-841178746da0/@@download/4DNFIN61HEL4.bw", "filename":"4DNFIN61HEL4", "status":"to be uploaded by workflow", "upload_key":"7cdb8876-385f-4212-93bf-841178746da0/4DNFIN61HEL4.bw" } ], "extension":".bedGraph.gz", "secondary_file_extensions":[ ".bedGraph.gz.px2", ".bw" ], "secondary_file_formats":[ "bg_px2", "bw" ], "format":"bg", "upload_key":"7cdb8876-385f-4212-93bf-841178746da0/4DNFIN61HEL4.bedGraph.gz" } ], "file":[ { "file_format":{ "file_format":"bg", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "uuid":"d1312212-218e-4f61-aaf0-91f226248b2c", "@type":[ "FileFormat", "Item" ], "display_title":"bg", "@id":"/file-formats/bg/" }, "file_size":3550525, "experiments":[ { "uuid":"b2e1dd76-e8de-48d8-80f5-339c69094aaa", "@id":"/experiments-repliseq/4DNEXN62FHTX/", "experiment_sets":[ { "uuid":"b6b8efc9-07c4-47f0-9f97-8d6a1c5f179c", "@id":"/experiment-set-replicates/4DNESUJC9Y83/" }, { "uuid":"d4aef6dd-f83b-4659-b0f3-88af71357920", "@id":"/experiment-sets/4DNESEJCRVNR/" } ] } ], "href":"/files-processed/4DNFIN61HEL4/@@download/4DNFIN61HEL4.bedGraph.gz", "@id":"/files-processed/4DNFIN61HEL4/", "status":"released", "file_type":"counts", "accession":"4DNFIN61HEL4", "uuid":"7cdb8876-385f-4212-93bf-841178746da0", "@type":[ "FileProcessed", "File", "Item" ], "description":"read counts per 5 kb bin, unfiltered, unnormalized", "experiment_sets":[ ], "display_title":"4DNFIN61HEL4.bedGraph.gz" } ] }, "target":[ { "name":"count_bg" } ], "name":"count_bg", "meta":{ "global":true, "in_path":true, "type":"data file" } } ], "inputs":[ { "run_data":{ "type":"input", "meta":[ { "workflow_argument_name":"fastq", "ordinal":1, "dimension":"0" } ], "file":[ { "file_format":{ "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "uuid":"c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type":[ "FileFormat", "Item" ], "display_title":"fastq", "file_format":"fastq", "@id":"/file-formats/fastq/" }, "file_size":409756358, "experiments":[ { "uuid":"b2e1dd76-e8de-48d8-80f5-339c69094aaa", "@id":"/experiments-repliseq/4DNEXN62FHTX/", "experiment_sets":[ { "uuid":"b6b8efc9-07c4-47f0-9f97-8d6a1c5f179c", "@id":"/experiment-set-replicates/4DNESUJC9Y83/" }, { "uuid":"d4aef6dd-f83b-4659-b0f3-88af71357920", "@id":"/experiment-sets/4DNESEJCRVNR/" } ] } ], "href":"/files-fastq/4DNFIPL7BXYA/@@download/4DNFIPL7BXYA.fastq.gz", "@id":"/files-fastq/4DNFIPL7BXYA/", "status":"released", "quality_metric":{ "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "overall_quality_status":"PASS", "uuid":"232d5ef4-c326-464e-be32-f8ba7c700bc5", "@type":[ "QualityMetricFastqc", "QualityMetric", "Item" ], "display_title":"QualityMetricFastqc from 2017-09-01", "Total Sequences":8985438, "url":"https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIPL7BXYA/fastqc_report.html", "@id":"/quality-metrics-fastqc/232d5ef4-c326-464e-be32-f8ba7c700bc5/", "Sequence length":"50" }, "file_type":"reads", "accession":"4DNFIPL7BXYA", "uuid":"d1d3531f-e06a-4b0a-aae1-d0130b965730", "@type":[ "FileFastq", "File", "Item" ], "filename":"H1_R2_L.fastq.gz", "display_title":"4DNFIPL7BXYA.fastq.gz" } ] }, "name":"fastq", "meta":{ "global":true, "in_path":true, "type":"data file" }, "source":[ { "for_file":"/files-fastq/4DNFIPL7BXYA/", "name":"fastq" } ] }, { "run_data":{ "type":"input", "meta":[ { "workflow_argument_name":"chromsizes", "ordinal":1, "dimension":"0" } ], "file":[ { "file_format":{ "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "uuid":"d13d06cf-218e-4f61-55f0-93f226248b2c", "@type":[ "FileFormat", "Item" ], "@id":"/file-formats/chromsizes/", "file_format":"chromsizes", "display_title":"chromsizes" }, "file_size":365, "experiments":[ ], "href":"/files-reference/4DNFI823LSII/@@download/4DNFI823LSII.chrom.sizes", "@id":"/files-reference/4DNFI823LSII/", "status":"released", "file_type":"other", "accession":"4DNFI823LSII", "uuid":"4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "@type":[ "FileReference", "File", "Item" ], "description":"Chromosome sizes file for the human genome build hg38. Only the assembled chromosomes are included; unlocalized or unplaced contigs are excluded. ", "filename":"hg38.mainonly.chrom.sizes", "display_title":"4DNFI823LSII.chrom.sizes" } ] }, "name":"chromsizes", "meta":{ "global":true, "in_path":true, "type":"reference file" }, "source":[ { "for_file":"/files-reference/4DNFI823LSII/", "name":"chromsizes" } ] }, { "run_data":{ "type":"input", "meta":[ { "workflow_argument_name":"bwaIndex", "ordinal":1, "dimension":"0" } ], "file":[ { "file_format":{ "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "file_format":"bwaIndex", "uuid":"d13d06cf-218e-4f61-55f0-91f226248b2c", "@type":[ "FileFormat", "Item" ], "@id":"/file-formats/bwaIndex/", "display_title":"bwaIndex" }, "file_size":3445308903, "experiments":[ ], "href":"/files-reference/4DNFIZQZ39L9/@@download/4DNFIZQZ39L9.bwaIndex.tgz", "@id":"/files-reference/4DNFIZQZ39L9/", "status":"released", "file_type":"genome index", "accession":"4DNFIZQZ39L9", "uuid":"1f53df95-4cf3-41cc-971d-81bb16c486dd", "@type":[ "FileReference", "File", "Item" ], "description":"This tar-gzipped file includes the bwa index for the human genome build GRCh38. We use the UCSC hg38 version of the genome, corresponsing to GRCh38/GCA_000001405.15 including the 25 assembled chromosomes (1-22, X, Y, M), the 127 unplaced contigs, the 42 unlocalized contigs, but excluding the 261 alternative haplotypes. The assembly also includes the Epstein-Barr virus (EBV) genome. This is the same reference as used by the ENCODE Consortium for data processing: https://www.encodeproject.org/data-standards/reference-sequences/ .", "filename":"hg38.bwaIndex.tgz", "display_title":"4DNFIZQZ39L9.bwaIndex.tgz" } ] }, "name":"bwaIndex", "meta":{ "global":true, "in_path":true, "type":"reference file" }, "source":[ { "for_file":"/files-reference/4DNFIZQZ39L9/", "name":"bwaIndex" } ] } ], "name":"/workflow-runs-awsem/f08d5cec-dbed-42c6-9507-aa9c4ab910ad/", "meta":{ "run_status":"complete", "analysis_step_types":[ "processing" ], "@type":[ "WorkflowRunAwsem", "WorkflowRun", "Item" ], "display_title":"repliseq-parta v13.1 run 2018-05-25 20:54:30.309699", "date_created":"2018-05-25T20:54:30.503169+00:00", "status":"released", "workflow":{ "uuid":"146da22a-502d-4500-bf57-a7cf0b4b2364", "steps":[ { "meta":{ "analysis_step_types":[ "adapter removal" ], "software_used":[ "97ffd707-b673-4184-a0f6-ca1dfc324067", "a5d01ff2-88b5-45c6-9c1d-f6c156248b43" ], "description":"Adapter removal according to the Repli-seq pipeline" }, "outputs":[ { "target":[ { "step":"align", "name":"fastq1" } ], "name":"out_clipped_fastq", "meta":{ "file_format":"fastq", "global":false, "cardinality":"single" } } ], "name":"clip", "inputs":[ { "name":"input_fastq", "meta":{ "file_format":"c13d06cf-218e-4f61-aaf0-91f226248b2c", "global":true, "type":"data file", "cardinality":"single" }, "source":[ { "name":"fastq" } ] } ] }, { "meta":{ "analysis_step_types":[ "alignment" ], "software_used":[ "5befdeda-66a8-43bc-a469-5a5e7248198e", "a5d01ff2-88b5-45c6-9c1d-f6c156248b43" ], "description":"Alignment according to the Repli-seq pipeline" }, "outputs":[ { "target":[ { "step":"filtersort", "name":"input_bam" } ], "name":"out_bam", "meta":{ "file_format":"bam", "global":false, "cardinality":"single" } } ], "name":"align", "inputs":[ { "name":"fastq1", "meta":{ "file_format":"c13d06cf-218e-4f61-aaf0-91f226248b2c", "global":false, "cardinality":"single" }, "source":[ { "step":"clip", "name":"out_clipped_fastq" } ] }, { "name":"bwa_index", "meta":{ "file_format":"d13d06cf-218e-4f61-55f0-91f226248b2c", "global":true, "type":"reference file", "cardinality":"single" }, "source":[ { "name":"bwaIndex" } ] }, { "name":"nThreads", "meta":{ "global":true, "type":"parameter", "cardinality":"single" }, "source":[ { "name":"nthreads" } ] } ] }, { "meta":{ "analysis_step_types":[ "filtering", "sorting" ], "software_used":[ "752e712f-4ebe-4335-a95e-53cd55a8a42f", "a5d01ff2-88b5-45c6-9c1d-f6c156248b43" ], "description":"Filtering and sorting according to the Repli-seq pipeline" }, "outputs":[ { "target":[ { "step":"dedup", "name":"input_bam" } ], "name":"out_filtered_sorted_bam", "meta":{ "file_format":"bam", "global":false, "cardinality":"single" } } ], "name":"filtersort", "inputs":[ { "name":"input_bam", "meta":{ "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "global":false, "cardinality":"single" }, "source":[ { "step":"align", "name":"out_bam" } ] }, { "name":"nthreads", "meta":{ "global":true, "type":"parameter", "cardinality":"single" }, "source":[ { "name":"nthreads" } ] }, { "name":"memperthread", "meta":{ "global":true, "type":"parameter", "cardinality":"single" }, "source":[ { "name":"memperthread" } ] } ] }, { "meta":{ "analysis_step_types":[ "duplicate removal" ], "software_used":[ "752e712f-4ebe-4335-a95e-53cd55a8a42f", "a5d01ff2-88b5-45c6-9c1d-f6c156248b43" ], "description":"PCR Duplicate removal according to the Repli-seq pipeline" }, "outputs":[ { "target":[ { "name":"filtered_sorted_deduped_bam" }, { "step":"count", "name":"input_bam" } ], "name":"out_deduped_bam", "meta":{ "file_format":"bam", "global":true, "type":"data file", "cardinality":"single" } }, { "target":[ { "name":"dedup_qc_report" } ], "name":"out_qc_report", "meta":{ "global":true, "type":"QC", "cardinality":"single" } } ], "name":"dedup", "inputs":[ { "name":"input_bam", "meta":{ "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "global":false, "cardinality":"single" }, "source":[ { "step":"filtersort", "name":"out_filtered_sorted_bam" } ] } ] }, { "meta":{ "analysis_step_types":[ "binning", "aggregation" ], "software_used":[ "13d47cb7-79d1-4472-8d6f-1e1263631b4e", "a5d01ff2-88b5-45c6-9c1d-f6c156248b43", "58c2eadd-7a15-4e8c-960f-9c7022af2bfc", "00eda937-3149-4252-8dc9-c27de59d75ed" ], "description":"Read aggregation according to the Repli-seq pipeline" }, "outputs":[ { "target":[ { "name":"count_bg" } ], "name":"out_count_bg", "meta":{ "file_format":"bg", "global":true, "type":"data file", "cardinality":"single" } } ], "name":"count", "inputs":[ { "name":"input_bam", "meta":{ "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "global":false, "type":"data file", "cardinality":"single" }, "source":[ { "step":"dedup", "name":"out_deduped_bam" } ] }, { "name":"chrsizes", "meta":{ "file_format":"d13d06cf-218e-4f61-55f0-93f226248b2c", "global":true, "type":"reference file", "cardinality":"single" }, "source":[ { "name":"chromsizes" } ] }, { "name":"winsize", "meta":{ "global":true, "type":"parameter", "cardinality":"single" }, "source":[ { "name":"winsize" } ] } ] } ], "@type":[ "Workflow", "Item" ], "@id":"/workflows/146da22a-502d-4500-bf57-a7cf0b4b2364/", "experiment_types":[ "Repli-seq" ], "category":[ "processing" ], "accession":"4DNWFBKH3JR1", "display_title":"Repli-seq data processing pipeline for alignment, filtering and counting v13.1 - 4DNWFBKH3JR1" }, "@id":"/workflow-runs-awsem/f08d5cec-dbed-42c6-9507-aa9c4ab910ad/" } }, { "outputs":[ { "run_data":{ "type":"input", "meta":[ { "extension":".bam", "type":"Output processed file", "format":"bam", "extra_files":null, "upload_key":"f24581c9-ed88-47d7-93c2-3bce1aa24dac/4DNFIMOR9IMU.bam" } ], "file":[ { "file_format":{ "file_format":"bam", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "@type":[ "FileFormat", "Item" ], "display_title":"bam", "@id":"/file-formats/bam/" }, "file_size":101077965, "experiments":[ { "uuid":"b2e1dd76-e8de-48d8-80f5-339c69094aaa", "@id":"/experiments-repliseq/4DNEXN62FHTX/", "experiment_sets":[ { "uuid":"b6b8efc9-07c4-47f0-9f97-8d6a1c5f179c", "@id":"/experiment-set-replicates/4DNESUJC9Y83/" }, { "uuid":"d4aef6dd-f83b-4659-b0f3-88af71357920", "@id":"/experiment-sets/4DNESEJCRVNR/" } ] } ], "href":"/files-processed/4DNFIMOR9IMU/@@download/4DNFIMOR9IMU.bam", "@id":"/files-processed/4DNFIMOR9IMU/", "status":"released", "quality_metric":{ "uuid":"80595046-0bfc-4d7f-b677-fe667e78da60", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "@type":[ "QualityMetricDedupqcRepliseq", "QualityMetric", "Item" ], "display_title":"QualityMetricDedupqcRepliseq from 2018-05-25", "@id":"/quality-metrics-dedupqc-repliseq/80595046-0bfc-4d7f-b677-fe667e78da60/" }, "file_type":"alignment", "accession":"4DNFIMOR9IMU", "uuid":"f24581c9-ed88-47d7-93c2-3bce1aa24dac", "@type":[ "FileProcessed", "File", "Item" ], "description":"This is an output file of the RepliSeq processing pipeline", "experiment_sets":[ ], "display_title":"4DNFIMOR9IMU.bam" } ] }, "target":[ { "name":"filtered_sorted_deduped_bam" } ], "name":"filtered_sorted_deduped_bam", "meta":{ "global":true, "in_path":true, "type":"data file" } }, { "run_data":{ "type":"input", "meta":[ { "type":"Output processed file", "extra_files":[ { "uuid":"ae2ab0d4-79f6-4e98-89a7-85bf45b382f7", "file_format":"bg_px2", "accession":"4DNFI4BSJRMF", "href":"/ae2ab0d4-79f6-4e98-89a7-85bf45b382f7/@@download/4DNFI4BSJRMF.bedGraph.gz.px2", "filename":"4DNFI4BSJRMF", "status":"to be uploaded by workflow", "upload_key":"ae2ab0d4-79f6-4e98-89a7-85bf45b382f7/4DNFI4BSJRMF.bedGraph.gz.px2" }, { "uuid":"ae2ab0d4-79f6-4e98-89a7-85bf45b382f7", "file_format":"bw", "accession":"4DNFI4BSJRMF", "href":"/ae2ab0d4-79f6-4e98-89a7-85bf45b382f7/@@download/4DNFI4BSJRMF.bw", "filename":"4DNFI4BSJRMF", "status":"to be uploaded by workflow", "upload_key":"ae2ab0d4-79f6-4e98-89a7-85bf45b382f7/4DNFI4BSJRMF.bw" } ], "extension":".bedGraph.gz", "secondary_file_extensions":[ ".bedGraph.gz.px2", ".bw" ], "secondary_file_formats":[ "bg_px2", "bw" ], "format":"bg", "upload_key":"ae2ab0d4-79f6-4e98-89a7-85bf45b382f7/4DNFI4BSJRMF.bedGraph.gz" } ], "file":[ { "file_format":{ "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "uuid":"d1312212-218e-4f61-aaf0-91f226248b2c", "@type":[ "FileFormat", "Item" ], "display_title":"bg", "file_format":"bg", "@id":"/file-formats/bg/" }, "file_size":3215994, "experiments":[ { "uuid":"b2e1dd76-e8de-48d8-80f5-339c69094aaa", "@id":"/experiments-repliseq/4DNEXN62FHTX/", "experiment_sets":[ { "uuid":"b6b8efc9-07c4-47f0-9f97-8d6a1c5f179c", "@id":"/experiment-set-replicates/4DNESUJC9Y83/" }, { "uuid":"d4aef6dd-f83b-4659-b0f3-88af71357920", "@id":"/experiment-sets/4DNESEJCRVNR/" } ] } ], "href":"/files-processed/4DNFI4BSJRMF/@@download/4DNFI4BSJRMF.bedGraph.gz", "@id":"/files-processed/4DNFI4BSJRMF/", "status":"released", "file_type":"counts", "accession":"4DNFI4BSJRMF", "uuid":"ae2ab0d4-79f6-4e98-89a7-85bf45b382f7", "@type":[ "FileProcessed", "File", "Item" ], "description":"read counts per 5 kb bin, unfiltered, unnormalized", "experiment_sets":[ ], "display_title":"4DNFI4BSJRMF.bedGraph.gz" } ] }, "target":[ { "name":"count_bg" } ], "name":"count_bg", "meta":{ "global":true, "in_path":true, "type":"data file" } } ], "inputs":[ { "run_data":{ "type":"input", "meta":[ { "workflow_argument_name":"fastq", "ordinal":1, "dimension":"0" } ], "file":[ { "file_format":{ "uuid":"c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format":"fastq", "@type":[ "FileFormat", "Item" ], "display_title":"fastq", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "@id":"/file-formats/fastq/" }, "file_size":108252021, "experiments":[ { "uuid":"b2e1dd76-e8de-48d8-80f5-339c69094aaa", "@id":"/experiments-repliseq/4DNEXN62FHTX/", "experiment_sets":[ { "uuid":"b6b8efc9-07c4-47f0-9f97-8d6a1c5f179c", "@id":"/experiment-set-replicates/4DNESUJC9Y83/" }, { "uuid":"d4aef6dd-f83b-4659-b0f3-88af71357920", "@id":"/experiment-sets/4DNESEJCRVNR/" } ] } ], "href":"/files-fastq/4DNFIPBQPYG5/@@download/4DNFIPBQPYG5.fastq.gz", "@id":"/files-fastq/4DNFIPBQPYG5/", "status":"released", "quality_metric":{ "uuid":"e27baac6-5ce2-467e-a4a8-c5fe24dc533b", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "Total Sequences":2206429, "@type":[ "QualityMetricFastqc", "QualityMetric", "Item" ], "Sequence length":"50", "overall_quality_status":"PASS", "url":"https://s3.amazonaws.com/elasticbe