UNPKG

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

Version:

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

584 lines (583 loc) 20 kB
[ { "meta":{ "description":"Parsing and sorting bam file", "software_used":[ { "name":"pairsamtools", "@id":"/softwares/58ed98d7-10d8-4c51-8166-4a813c62ef8c/", "uuid":"58ed98d7-10d8-4c51-8166-4a813c62ef8c", "status":"released", "display_title":"pairsamtools_eccd21", "@type":[ "Software", "Item" ], "title":"pairsamtools_eccd21", "source_url":"https://github.com/mirnylab/pairsamtools", "principals_allowed":{ "view":[ "system.Everyone" ], "edit":[ "group.admin" ] } } ], "analysis_step_types":[ "annotation", "sorting" ] }, "name":"pairsam-parse-sort", "inputs":[ { "meta":{ "type":"data file", "global":true, "cardinality":"single", "scatter": 1, "file_format":{ "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "@type":[ "FileFormat", "Item" ], "status":"released", "display_title":"bam", "@id":"/file-formats/bam/", "principals_allowed":{ "view":[ "system.Everyone" ], "edit":[ "group.admin" ] } } }, "name":"bam", "source":[ { "name":"input_bams" } ], "run_data":{ "file":[ "961f40f7-0e9a-4401-9f20-76326951e39a", "7680f713-e416-4230-8133-43c930ac36ff", "02cc6f4a-1d36-4211-ba74-3e7d75ad153a", "208fa0a8-6e9a-47d7-ab93-35c4a4e25ec9", "22de6751-4734-473e-92b3-936dae7d48f3", "29af847c-3e45-4a06-b364-110bc04e71c6", "97a3a3b9-6ed2-4a6d-9b29-c66848cec0d7", "0738949b-abc5-41ce-ab26-306d70d7abaa", "dda6ae1d-6882-40b0-8363-a0c7dff1aeca" ], "type":"input", "meta":[ { "ordinal":1, "dimension":"0" }, { "ordinal":2, "dimension":"0" }, { "ordinal":3, "dimension":"0" }, { "ordinal":4, "dimension":"0" }, { "ordinal":5, "dimension":"0" }, { "ordinal":6, "dimension":"0" }, { "ordinal":7, "dimension":"0" }, { "ordinal":8, "dimension":"0" }, { "ordinal":9, "dimension":"0" } ] } }, { "meta":{ "type":"reference file", "global":true, "cardinality":"single", "file_format":{ "uuid":"d13d06cf-218e-4f61-55f0-93f226248b2c", "@type":[ "FileFormat", "Item" ], "status":"released", "display_title":"chromsizes", "@id":"/file-formats/chromsizes/", "principals_allowed":{ "view":[ "system.Everyone" ], "edit":[ "group.admin" ] } } }, "name":"chromsize", "source":[ { "name":"chromsize" } ], "run_data":{ "file":[ "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9" ], "type":"input", "meta":[ { "ordinal":1, "dimension":"0" } ] } }, { "meta":{ "type":"parameter", "global":true, "cardinality":"single" }, "name":"Threads", "source":[ { "name":"nthreads_parse_sort" } ], "run_data":{ "value":[ "16" ], "type":"parameter", "meta":[ { "ordinal":1, "dimension":"0" } ] } } ], "outputs":[ { "meta":{ "type":"data file", "global":false, "cardinality":"single", "file_format":"pairsam" }, "name":"sorted_pairsam", "target":[ { "name":"input_pairsams", "step":"pairsam-merge" } ] } ] }, { "meta":{ "description":"Merging pairsam files", "software_used":[ { "name":"pairsamtools", "@id":"/softwares/58ed98d7-10d8-4c51-8166-4a813c62ef8c/", "uuid":"58ed98d7-10d8-4c51-8166-4a813c62ef8c", "status":"released", "display_title":"pairsamtools_eccd21", "@type":[ "Software", "Item" ], "title":"pairsamtools_eccd21", "source_url":"https://github.com/mirnylab/pairsamtools", "principals_allowed":{ "view":[ "system.Everyone" ], "edit":[ "group.admin" ] } } ], "analysis_step_types":[ "merging" ] }, "name":"pairsam-merge", "inputs":[ { "meta":{ "type":"data file", "global":false, "gather": 1, "cardinality":"array", "file_format":{ "uuid":"d13d06cf-218e-5f61-aaf0-91f226248b2c", "@type":[ "FileFormat", "Item" ], "status":"released", "display_title":"pairsam", "@id":"/file-formats/pairsam/", "principals_allowed":{ "view":[ "system.Everyone" ], "edit":[ "group.admin" ] } } }, "name":"input_pairsams", "source":[ { "name":"sorted_pairsam", "step":"pairsam-parse-sort" } ] }, { "meta":{ "type":"parameter", "global":true, "cardinality":"single" }, "name":"nThreads", "source":[ { "name":"nthreads_merge" } ], "run_data":{ "value":[ "16" ], "type":"parameter", "meta":[ { "ordinal":1, "dimension":"0" } ] } } ], "outputs":[ { "meta":{ "type":"data file", "global":false, "cardinality":"single", "file_format":"pairsam" }, "name":"merged_pairsam", "target":[ { "name":"input_pairsam", "step":"pairsam-markasdup" } ] } ] }, { "meta":{ "description":"Marking duplicates to pairsam file", "software_used":[ { "name":"pairsamtools", "@id":"/softwares/58ed98d7-10d8-4c51-8166-4a813c62ef8c/", "uuid":"58ed98d7-10d8-4c51-8166-4a813c62ef8c", "status":"released", "display_title":"pairsamtools_eccd21", "@type":[ "Software", "Item" ], "title":"pairsamtools_eccd21", "source_url":"https://github.com/mirnylab/pairsamtools", "principals_allowed":{ "view":[ "system.Everyone" ], "edit":[ "group.admin" ] } } ], "analysis_step_types":[ "filter" ] }, "name":"pairsam-markasdup", "inputs":[ { "meta":{ "type":"data file", "global":false, "cardinality":"single", "file_format":{ "uuid":"d13d06cf-218e-5f61-aaf0-91f226248b2c", "@type":[ "FileFormat", "Item" ], "status":"released", "display_title":"pairsam", "@id":"/file-formats/pairsam/", "principals_allowed":{ "view":[ "system.Everyone" ], "edit":[ "group.admin" ] } } }, "name":"input_pairsam", "source":[ { "name":"merged_pairsam", "step":"pairsam-merge" } ] } ], "outputs":[ { "meta":{ "type":"data file", "global":false, "cardinality":"single", "file_format":"pairsam" }, "name":"dupmarked_pairsam", "target":[ { "name":"input_pairsam", "step":"pairsam-filter" } ] } ] }, { "meta":{ "description":"Filtering duplicate and invalid reads", "software_used":[ { "name":"pairsamtools", "@id":"/softwares/58ed98d7-10d8-4c51-8166-4a813c62ef8c/", "uuid":"58ed98d7-10d8-4c51-8166-4a813c62ef8c", "status":"released", "display_title":"pairsamtools_eccd21", "@type":[ "Software", "Item" ], "title":"pairsamtools_eccd21", "source_url":"https://github.com/mirnylab/pairsamtools", "principals_allowed":{ "view":[ "system.Everyone" ], "edit":[ "group.admin" ] } } ], "analysis_step_types":[ "filter", "file format conversion" ] }, "name":"pairsam-filter", "inputs":[ { "meta":{ "type":"data file", "global":false, "cardinality":"single", "file_format":{ "uuid":"d13d06cf-218e-5f61-aaf0-91f226248b2c", "@type":[ "FileFormat", "Item" ], "status":"released", "display_title":"pairsam", "@id":"/file-formats/pairsam/", "principals_allowed":{ "view":[ "system.Everyone" ], "edit":[ "group.admin" ] } } }, "name":"input_pairsam", "source":[ { "name":"dupmarked_pairsam", "step":"pairsam-markasdup" } ] }, { "meta":{ "type":"reference file", "global":true, "cardinality":"single", "file_format":{ "uuid":"d13d06cf-218e-4f61-55f0-93f226248b2c", "@type":[ "FileFormat", "Item" ], "status":"released", "display_title":"chromsizes", "@id":"/file-formats/chromsizes/", "principals_allowed":{ "view":[ "system.Everyone" ], "edit":[ "group.admin" ] } } }, "name":"chromsize", "source":[ { "name":"chromsize" } ], "run_data":{ "file":[ "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9" ], "type":"input", "meta":[ { "ordinal":1, "dimension":"0" } ] } } ], "outputs":[ { "meta":{ "type":"data file", "global":true, "cardinality":"single", "file_format":"bam" }, "name":"lossless_bamfile", "target":[ { "name":"annotated_bam" } ], "run_data":{ "file":[ "13df1f34-672a-4721-977a-27bda15f3c26" ], "type":"output", "meta":[ { "format":"bam", "extension":".bam", "upload_key":"13df1f34-672a-4721-977a-27bda15f3c26/4DNFIQP64RT3.bam", "extra_files":[ ] } ] } }, { "meta":{ "type":"data file", "global":true, "cardinality":"single", "file_format":"pairs" }, "name":"filtered_pairs", "target":[ { "name":"filtered_pairs" } ], "run_data":{ "file":[ "0401edff-028d-48cf-b3a9-ac58f35a4a3b" ], "type":"output", "meta":[ { "format":"pairs", "extension":".pairs.gz", "upload_key":"0401edff-028d-48cf-b3a9-ac58f35a4a3b/4DNFILR6CKEJ.pairs.gz", "extra_files":[ { "href":"/0401edff-028d-48cf-b3a9-ac58f35a4a3b/@@download/4DNFILR6CKEJ.pairs.gz.px2", "uuid":"0401edff-028d-48cf-b3a9-ac58f35a4a3b", "status":"to be uploaded by workflow", "filename":"4DNFILR6CKEJ", "accession":"4DNFILR6CKEJ", "upload_key":"0401edff-028d-48cf-b3a9-ac58f35a4a3b/4DNFILR6CKEJ.pairs.gz.px2", "file_format":"pairs_px2" } ], "secondary_file_formats":[ "pairs_px2" ], "secondary_file_extensions":[ ".pairs.gz.px2" ] } ] } } ] } ]