UNPKG

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

Version:

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

1,122 lines (1,119 loc) 543 kB
[ { "name":"/workflow-runs-awsem/9ef1362f-a319-4ed2-93f7-720a765e5599/", "meta":{ "analysis_step_types":[ "processing" ], "@type":[ "WorkflowRunAwsem", "WorkflowRun", "Item" ], "@id":"/workflow-runs-awsem/9ef1362f-a319-4ed2-93f7-720a765e5599/", "date_created":"2019-11-25T06:01:10.146193+00:00", "display_title":"workflow_add-readgroups-check v11 run 2019-11-25 06:01:10.109581", "workflow":{ "@type":[ "Workflow", "Item" ], "@id":"/workflows/1ebf697c-949d-46b2-b9a4-8b1a7699ef1f/", "experiment_types":[ ], "accession":"GAPWFBN35DT2", "steps":[ { "name":"add-readgroups", "meta":{ "software_used":[ "d7ac4c75-e133-4a8e-a19e-b7e87873cc16" ], "analysis_step_types":[ "Add read groups to bam input file" ] }, "outputs":[ { "name":"bam_w_readgroups", "target":[ { "name":"bam_w_readgroups", "step":"integrity-check" } ], "meta":{ "cardinality":"single", "file_format":"bam", "type":"data file", "global":true } } ], "inputs":[ { "name":"input_bam", "meta":{ "cardinality":"single", "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "type":"data file", "global":true }, "source":[ { "name":"input_bam" } ] }, { "name":"sample_name", "meta":{ "cardinality":"single", "global":true, "type":"parameter" }, "source":[ { "name":"sample_name" } ] }, { "name":"nthreads", "meta":{ "cardinality":"single", "global":true, "type":"parameter" }, "source":[ { "name":"nthreads" } ] } ] }, { "name":"integrity-check", "meta":{ "software_used":[ "3f2d3b0e-0365-4212-9468-c16ad9531c4d" ], "analysis_step_types":[ "Check integrity of output file" ] }, "outputs":[ { "name":"bam_w_readgroups-check", "target":[ { "name":"bam_w_readgroups-check" } ], "meta":{ "cardinality":"single", "global":true, "type":"QC" } } ], "inputs":[ { "name":"bam_w_readgroups", "meta":{ "cardinality":"single", "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "type":"data file", "global":false }, "source":[ { "name":"bam_w_readgroups", "step":"add-readgroups" } ] }, { "name":"count", "meta":{ "cardinality":"single", "global":true, "type":"parameter" }, "source":[ { "name":"count" } ] } ] } ], "display_title":"Add read groups plus output integrity-check - GAPWFBN35DT2", "category":[ "processing" ], "uuid":"1ebf697c-949d-46b2-b9a4-8b1a7699ef1f" }, "run_status":"complete", "status":"in review" }, "outputs":[ { "name":"bam_w_readgroups", "target":[ { "name":"bam_w_readgroups" }, { "name":"input_bam", "for_file":"/files-processed/GAPFI9PUMN3F/", "step":"/workflow-runs-awsem/1acf44d1-d7ce-42be-ba39-31d3c47a93eb/" }, { "name":"input_bam", "for_file":"/files-processed/GAPFI9PUMN3F/", "step":"/workflow-runs-awsem/1acf44d1-d7ce-42be-ba39-31d3c47a93eb/" } ], "run_data":{ "file":[ { "file_format":{ "file_format":"bam", "@type":[ "FileFormat", "Item" ], "@id":"/file-formats/bam/", "principals_allowed":{ "view":[ "group.admin", "group.read-only-admin", "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "project.12a92962-8265-4fc0-b2f8-cf14f05db58b", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ] }, "display_title":"bam", "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c" }, "quality_metric":{ "display_title":"QualityMetricBamcheck from 2019-11-25", "@type":[ "QualityMetricBamcheck", "QualityMetric", "Item" ], "@id":"/quality-metrics-bamcheck/38d19a8f-eda7-44db-a3e6-c2c23cc0c43a/", "principals_allowed":{ "view":[ "group.admin", "group.read-only-admin", "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "project.12a92962-8265-4fc0-b2f8-cf14f05db58b", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ] }, "uuid":"38d19a8f-eda7-44db-a3e6-c2c23cc0c43a" }, "accession":"GAPFI9PUMN3F", "file_size":110764558680, "display_title":"GAPFI9PUMN3F.bam", "description":"Intermediate alignment file", "uuid":"6744d4c8-a0a2-4619-ada4-1f68991fb994", "status":"uploaded", "@type":[ "FileProcessed", "File", "Item" ], "@id":"/files-processed/GAPFI9PUMN3F/", "href":"/files-processed/GAPFI9PUMN3F/@@download/GAPFI9PUMN3F.bam", "file_type":"intermediate file" } ], "meta":[ { "format":"/file-formats/bam/", "type":"Output processed file", "upload_key":"6744d4c8-a0a2-4619-ada4-1f68991fb994/GAPFI9PUMN3F.bam" } ], "type":"input" }, "meta":{ "global":true, "in_path":true, "type":"data file" } }, { "name":"bam_w_readgroups-check", "target":[ { "name":"bam_w_readgroups-check" } ], "run_data":{ "file":[ { "@type":[ "QualityMetricBamcheck", "QualityMetric", "Item" ], "@id":"/quality-metrics-bamcheck/38d19a8f-eda7-44db-a3e6-c2c23cc0c43a/", "accession":null, "display_title":"QualityMetricBamcheck from 2019-11-25", "uuid":"38d19a8f-eda7-44db-a3e6-c2c23cc0c43a", "status":"in review" } ], "meta":[ { "type":"Output QC file" } ], "type":"input" }, "meta":{ "global":true, "in_path":false, "type":"QC" } } ], "inputs":[ { "name":"input_bam", "meta":{ "in_path":true, "global":true, "type":"data file" }, "source":[ { "name":"raw_bam", "workflow":"/workflows/9e094699-561b-4396-8d6a-ffc45f98c5e1/", "for_file":"/files-processed/GAPFI5V1GIRY/", "step":"/workflow-runs-awsem/d05d398a-0887-4de3-a4cd-a2151b8863f0/" } ], "run_data":{ "file":[ { "file_format":{ "file_format":"bam", "@type":[ "FileFormat", "Item" ], "@id":"/file-formats/bam/", "principals_allowed":{ "view":[ "group.admin", "group.read-only-admin", "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "project.12a92962-8265-4fc0-b2f8-cf14f05db58b", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ] }, "display_title":"bam", "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c" }, "quality_metric":{ "display_title":"QualityMetricBamcheck from 2019-11-25", "@type":[ "QualityMetricBamcheck", "QualityMetric", "Item" ], "@id":"/quality-metrics-bamcheck/0cbb2e67-0c45-40a0-9aa0-837ff5dec1a1/", "principals_allowed":{ "view":[ "group.admin", "group.read-only-admin", "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "project.12a92962-8265-4fc0-b2f8-cf14f05db58b", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ] }, "uuid":"0cbb2e67-0c45-40a0-9aa0-837ff5dec1a1" }, "accession":"GAPFI5V1GIRY", "file_size":109338750489, "display_title":"GAPFI5V1GIRY.bam", "description":"Intermediate alignment file", "uuid":"eca5a9ac-f00a-4279-aab9-3f4ed17015c9", "status":"uploaded", "@type":[ "FileProcessed", "File", "Item" ], "@id":"/files-processed/GAPFI5V1GIRY/", "href":"/files-processed/GAPFI5V1GIRY/@@download/GAPFI5V1GIRY.bam", "file_type":"intermediate file" } ], "meta":[ { "dimension":"0", "workflow_argument_name":"input_bam", "ordinal":1 } ], "type":"input" } } ] }, { "name":"/workflow-runs-awsem/1acf44d1-d7ce-42be-ba39-31d3c47a93eb/", "meta":{ "analysis_step_types":[ "processing" ], "@type":[ "WorkflowRunAwsem", "WorkflowRun", "Item" ], "@id":"/workflow-runs-awsem/1acf44d1-d7ce-42be-ba39-31d3c47a93eb/", "date_created":"2019-11-25T10:01:28.917978+00:00", "display_title":"workflow_picard-MarkDuplicates-check v11 run 2019-11-25 10:01:28.882673", "workflow":{ "@type":[ "Workflow", "Item" ], "@id":"/workflows/beb2b340-94ee-4afe-b4e3-66caaf063397/", "experiment_types":[ ], "accession":"GAPWFLNQ7XTG", "steps":[ { "name":"MarkDuplicates", "meta":{ "software_used":[ "586cef39-6505-4bf6-920a-4b26a500d210" ], "analysis_step_types":[ "Mark duplicates in bam input file" ] }, "outputs":[ { "name":"dupmarked_bam", "meta":{ "file_format":"bam", "global":true, "type":"data file", "cardinality":"single" }, "target":[ { "name":"dupmarked_bam", "step":"integrity-check" } ] }, { "name":"duplicate_metrics", "meta":{ "file_format":"txt", "global":true, "type":"data file", "cardinality":"single" }, "target":[ { "name":"duplicate_metrics" } ] } ], "inputs":[ { "name":"input_bam", "meta":{ "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "global":true, "type":"data file", "cardinality":"single" }, "source":[ { "name":"input_bam" } ] }, { "name":"xmx", "meta":{ "global":true, "cardinality":"single", "type":"parameter" }, "source":[ { "name":"xmx" } ] }, { "name":"xms", "meta":{ "global":true, "cardinality":"single", "type":"parameter" }, "source":[ { "name":"xms" } ] }, { "name":"max_records_in_ram", "meta":{ "global":true, "cardinality":"single", "type":"parameter" }, "source":[ { "name":"max_records_in_ram" } ] }, { "name":"duplicate_pixel_distance", "meta":{ "global":true, "cardinality":"single", "type":"parameter" }, "source":[ { "name":"duplicate_pixel_distance" } ] } ] }, { "name":"integrity-check", "meta":{ "software_used":[ "3f2d3b0e-0365-4212-9468-c16ad9531c4d" ], "analysis_step_types":[ "Check integrity of output file" ] }, "outputs":[ { "name":"dupmarked_bam-check", "meta":{ "global":true, "cardinality":"single", "type":"report" }, "target":[ { "name":"dupmarked_bam-check" } ] } ], "inputs":[ { "name":"dupmarked_bam", "meta":{ "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "global":false, "type":"data file", "cardinality":"single" }, "source":[ { "name":"dupmarked_bam", "step":"MarkDuplicates" } ] }, { "name":"count", "meta":{ "global":true, "cardinality":"single", "type":"parameter" }, "source":[ { "name":"count" } ] } ] } ], "display_title":"Mark duplicates plus output integrity-check - GAPWFLNQ7XTG", "category":[ "processing" ], "uuid":"beb2b340-94ee-4afe-b4e3-66caaf063397" }, "run_status":"complete", "status":"in review" }, "outputs":[ { "name":"dupmarked_bam", "target":[ { "name":"dupmarked_bam" }, { "name":"input_bam", "for_file":"/files-processed/GAPFIQHUBRKU/", "step":"/workflow-runs-awsem/2be2ec26-c846-48bd-9e61-4ebdca8a631a/" }, { "name":"input_bam", "for_file":"/files-processed/GAPFIQHUBRKU/", "step":"/workflow-runs-awsem/2be2ec26-c846-48bd-9e61-4ebdca8a631a/" }, { "name":"input_bam", "for_file":"/files-processed/GAPFIQHUBRKU/", "step":"/workflow-runs-awsem/2be2ec26-c846-48bd-9e61-4ebdca8a631a/" } ], "run_data":{ "file":[ { "file_format":{ "file_format":"bam", "@type":[ "FileFormat", "Item" ], "@id":"/file-formats/bam/", "principals_allowed":{ "view":[ "group.admin", "group.read-only-admin", "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "project.12a92962-8265-4fc0-b2f8-cf14f05db58b", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ] }, "display_title":"bam", "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c" }, "quality_metric":{ "display_title":"QualityMetricBamcheck from 2019-11-25", "@type":[ "QualityMetricBamcheck", "QualityMetric", "Item" ], "@id":"/quality-metrics-bamcheck/85de219f-42ae-4ac2-b7ad-62b7d381baed/", "principals_allowed":{ "view":[ "group.admin", "group.read-only-admin", "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "project.12a92962-8265-4fc0-b2f8-cf14f05db58b", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ] }, "uuid":"85de219f-42ae-4ac2-b7ad-62b7d381baed" }, "accession":"GAPFIQHUBRKU", "file_size":113357235025, "display_title":"GAPFIQHUBRKU.bam", "description":"Intermediate alignment file", "uuid":"3999a31d-d15d-433e-8bdf-88150fbfcbd4", "status":"uploaded", "@type":[ "FileProcessed", "File", "Item" ], "@id":"/files-processed/GAPFIQHUBRKU/", "href":"/files-processed/GAPFIQHUBRKU/@@download/GAPFIQHUBRKU.bam", "file_type":"intermediate file" } ], "meta":[ { "format":"/file-formats/bam/", "type":"Output processed file", "upload_key":"3999a31d-d15d-433e-8bdf-88150fbfcbd4/GAPFIQHUBRKU.bam" } ], "type":"input" }, "meta":{ "global":true, "in_path":true, "type":"data file" } }, { "name":"duplicate_metrics", "target":[ { "name":"duplicate_metrics" } ], "run_data":{ "file":[ { "file_format":{ "file_format":"txt", "@type":[ "FileFormat", "Item" ], "@id":"/file-formats/txt/", "principals_allowed":{ "view":[ "group.admin", "group.read-only-admin", "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "project.12a92962-8265-4fc0-b2f8-cf14f05db58b", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ] }, "display_title":"txt", "uuid":"0cd4e777-a596-4927-95c8-b07716121aa3" }, "@type":[ "FileProcessed", "File", "Item" ], "@id":"/files-processed/GAPFIAST6ER2/", "file_size":3520, "accession":"GAPFIAST6ER2", "display_title":"GAPFIAST6ER2.txt", "uuid":"1625a872-1546-42f7-9689-b77fa0d1d25f", "href":"/files-processed/GAPFIAST6ER2/@@download/GAPFIAST6ER2.txt", "status":"uploaded" } ], "meta":[ { "format":"/file-formats/txt/", "type":"Output processed file", "upload_key":"1625a872-1546-42f7-9689-b77fa0d1d25f/GAPFIAST6ER2.txt" } ], "type":"input" }, "meta":{ "global":true, "in_path":false, "type":"data file" } }, { "name":"dupmarked_bam-check", "target":[ { "name":"dupmarked_bam-check" } ], "run_data":{ "file":[ { "@type":[ "QualityMetricBamcheck", "QualityMetric", "Item" ], "@id":"/quality-metrics-bamcheck/85de219f-42ae-4ac2-b7ad-62b7d381baed/", "accession":null, "display_title":"QualityMetricBamcheck from 2019-11-25", "uuid":"85de219f-42ae-4ac2-b7ad-62b7d381baed", "status":"in review" } ], "meta":[ { "type":"Output QC file" } ], "type":"input" }, "meta":{ "global":true, "in_path":false, "type":"report" } } ], "inputs":[ { "name":"input_bam", "meta":{ "in_path":true, "global":true, "type":"data file" }, "source":[ { "name":"bam_w_readgroups", "workflow":"/workflows/1ebf697c-949d-46b2-b9a4-8b1a7699ef1f/", "for_file":"/files-processed/GAPFI9PUMN3F/", "step":"/workflow-runs-awsem/9ef1362f-a319-4ed2-93f7-720a765e5599/" } ], "run_data":{ "file":[ { "file_format":{ "file_format":"bam", "@type":[ "FileFormat", "Item" ], "@id":"/file-formats/bam/", "principals_allowed":{ "view":[ "group.admin", "group.read-only-admin", "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "project.12a92962-8265-4fc0-b2f8-cf14f05db58b", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ] }, "display_title":"bam", "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c" }, "quality_metric":{ "display_title":"QualityMetricBamcheck from 2019-11-25", "@type":[ "QualityMetricBamcheck", "QualityMetric", "Item" ], "@id":"/quality-metrics-bamcheck/38d19a8f-eda7-44db-a3e6-c2c23cc0c43a/", "principals_allowed":{ "view":[ "group.admin", "group.read-only-admin", "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "project.12a92962-8265-4fc0-b2f8-cf14f05db58b", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ] }, "uuid":"38d19a8f-eda7-44db-a3e6-c2c23cc0c43a" }, "accession":"GAPFI9PUMN3F", "file_size":110764558680, "display_title":"GAPFI9PUMN3F.bam", "description":"Intermediate alignment file", "uuid":"6744d4c8-a0a2-4619-ada4-1f68991fb994", "status":"uploaded", "@type":[ "FileProcessed", "File", "Item" ], "@id":"/files-processed/GAPFI9PUMN3F/", "href":"/files-processed/GAPFI9PUMN3F/@@download/GAPFI9PUMN3F.bam", "file_type":"intermediate file" } ], "meta":[ { "dimension":"0", "workflow_argument_name":"input_bam", "ordinal":1 } ], "type":"input" } } ] }, { "name":"/workflow-runs-awsem/2be2ec26-c846-48bd-9e61-4ebdca8a631a/", "meta":{ "analysis_step_types":[ "processing" ], "@type":[ "WorkflowRunAwsem", "WorkflowRun", "Item" ], "@id":"/workflow-runs-awsem/2be2ec26-c846-48bd-9e61-4ebdca8a631a/", "date_created":"2019-11-25T21:01:26.578249+00:00", "display_title":"workflow_sort-bam-check v11 run 2019-11-25 21:01:26.551370", "workflow":{ "@type":[ "Workflow", "Item" ], "@id":"/workflows/560f5194-cd3a-4799-9b1a-6a2d2c371c89/", "experiment_types":[ ], "accession":"GAPWFIFWUPJP", "steps":[ { "name":"sort", "meta":{ "software_used":[ "3f2d3b0e-0365-4212-9468-c16ad9531c4d" ], "analysis_step_types":[ "Sort bam input file" ] }, "outputs":[ { "name":"sorted_bam", "meta":{ "file_format":"bam", "global":true, "type":"data file", "cardinality":"single" }, "target":[ { "name":"sorted_bam", "step":"integrity-check" } ] } ], "inputs":[ { "name":"input_bam", "meta":{ "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "global":true, "type":"data file", "cardinality":"single" }, "source":[ { "name":"input_bam" } ] }, { "name":"max_memory", "meta":{ "global":true, "cardinality":"single", "type":"parameter" }, "source":[ { "name":"max_memory" } ] }, { "name":"nthreads", "meta":{ "global":true, "cardinality":"single", "type":"parameter" }, "source":[ { "name":"nthreads" } ] } ] }, { "name":"integrity-check", "meta":{ "software_used":[ "3f2d3b0e-0365-4212-9468-c16ad9531c4d" ], "analysis_step_types":[ "Check integrity of output file" ] }, "outputs":[ { "name":"sorted_bam-check", "meta":{ "global":true, "cardinality":"single", "type":"QC" }, "target":[ { "name":"sorted_bam-check" } ] } ], "inputs":[ { "name":"sorted_bam", "meta":{ "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "global":false, "type":"data file", "cardinality":"single" }, "source":[ { "name":"sorted_bam", "step":"sort" } ] }, { "name":"count", "meta":{ "global":true, "cardinality":"single", "type":"parameter" }, "source":[ { "name":"count" } ] } ] } ], "display_title":"Sort bam file plus output integrity-check - GAPWFIFWUPJP", "category":[ "processing" ], "uuid":"560f5194-cd3a-4799-9b1a-6a2d2c371c89" }, "run_status":"complete", "status":"in review" }, "outputs":[ { "name":"sorted_bam", "target":[ { "name":"sorted_bam" }, { "name":"input_bam", "for_file":"/files-processed/GAPFISSWY513/", "step":"/workflow-runs-awsem/5c565340-5f12-4d30-b043-0e4fadcd71f5/" }, { "name":"input_bam", "for_file":"/files-processed/GAPFISSWY513/", "step":"/workflow-runs-awsem/843f2c0d-084e-4f2a-bf3b-693f3dd5a406/" }, { "name":"input_bam", "for_file":"/files-processed/GAPFISSWY513/", "step":"/workflow-runs-awsem/5c565340-5f12-4d30-b043-0e4fadcd71f5/" }, { "name":"input_bam", "for_file":"/files-processed/GAPFISSWY513/", "step":"/workflow-runs-awsem/843f2c0d-084e-4f2a-bf3b-693f3dd5a406/" } ], "run_data":{ "file":[ { "file_format":{ "file_format":"bam", "@type":[ "FileFormat", "Item" ], "@id":"/file-formats/bam/", "principals_allowed":{ "view":[ "group.admin", "group.read-only-admin", "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "project.12a92962-8265-4fc0-b2f8-cf14f05db58b", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ] }, "display_title":"bam", "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c" }, "quality_metric":{ "display_title":"QualityMetricBamcheck from 2019-11-25", "@type":[ "QualityMetricBamcheck", "QualityMetric", "Item" ], "@id":"/quality-metrics-bamcheck/ded50f6d-a746-466c-abf6-7715fba65da6/", "uuid":"ded50f6d-a746-466c-abf6-7715fba65da6", "principals_allowed":{ "view":[ "group.admin", "group.