[ { "name":"/workflow-runs-awsem/d353e726-2a47-4e93-b1f4-cfa7037ee3bc/", "inputs":[ { "name":"fastq_R1", "source":[ { "name":"fastq_R1", "for_file":"/files-fastq/4DNFIW2ZKW3E/" } ], "run_data":{ "meta":[ { "workflow_argument_name":"fastq_R1", "ordinal":1, "dimension":"0" } ], "file":[ { "accession":"4DNFIW2ZKW3E", "href":"/files-fastq/4DNFIW2ZKW3E/@@download/4DNFIW2ZKW3E.fastq.gz", "uuid":"557a0497-e24f-44b8-9c9b-0aae5a54d1f9", "file_size":75137372363, "status":"uploaded", "file_type":"reads", "file_format":{ "file_format":"fastq", "@id":"/file-formats/fastq/", "uuid":"c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "@type":[ "FileFormat", "Item" ], "display_title":"fastq" }, "@id":"/files-fastq/4DNFIW2ZKW3E/", "experiments":[ { "experiment_sets":[ { "@id":"/experiment-set-replicates/4DNESNRXSDZB/", "uuid":"e6211c0c-5382-4026-a41a-a442af0163aa" } ], "@id":"/experiments-seq/4DNEXBT1CT94/", "uuid":"cd049338-8856-4a37-b2ca-4c81aaf52903" } ], "filename":"886794-UDN992716-D_R1.fastq.gz", "@type":[ "FileFastq", "File", "Item" ], "display_title":"4DNFIW2ZKW3E.fastq.gz", "quality_metric":{ "Sequence length":"35-150", "principals_allowed":{ "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ], "view":[ "award.b0b9c607-f8b4-4f02-93f4-9895b461334b", "group.admin", "group.read-only-admin", "lab.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "remoteuser.EMBED", "remoteuser.INDEXER" ] }, "Total Sequences":905396386, "overall_quality_status":"PASS", "@id":"/quality-metrics-fastqc/33882bdd-0656-4fd7-a987-efc65b72eb97/", "uuid":"33882bdd-0656-4fd7-a987-efc65b72eb97", "url":"https://s3.amazonaws.com/elasticbeanstalk-fourfront-webdev-wfoutput/4DNFIW2ZKW3E/fastqc_report.html", "@type":[ "QualityMetricFastqc", "QualityMetric", "Item" ], "display_title":"QualityMetricFastqc from 2019-08-13" } } ], "type":"input" }, "meta":{ "global":true, "in_path":true, "type":"data file" } }, { "name":"fastq_R2", "source":[ { "name":"fastq_R2", "for_file":"/files-fastq/4DNFIDA6Q5J4/" } ], "run_data":{ "meta":[ { "workflow_argument_name":"fastq_R2", "ordinal":1, "dimension":"0" } ], "file":[ { "accession":"4DNFIDA6Q5J4", "href":"/files-fastq/4DNFIDA6Q5J4/@@download/4DNFIDA6Q5J4.fastq.gz", "uuid":"37eb8e13-8052-4e6f-9fcc-46058865aa05", "file_size":78445497678, "status":"uploaded", "file_type":"reads", "file_format":{ "file_format":"fastq", "@id":"/file-formats/fastq/", "uuid":"c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "@type":[ "FileFormat", "Item" ], "display_title":"fastq" }, "@id":"/files-fastq/4DNFIDA6Q5J4/", "experiments":[ { "experiment_sets":[ { "@id":"/experiment-set-replicates/4DNESNRXSDZB/", "uuid":"e6211c0c-5382-4026-a41a-a442af0163aa" } ], "@id":"/experiments-seq/4DNEXBT1CT94/", "uuid":"cd049338-8856-4a37-b2ca-4c81aaf52903" } ], "filename":"886794-UDN992716-D_R2.fastq.gz", "@type":[ "FileFastq", "File", "Item" ], "display_title":"4DNFIDA6Q5J4.fastq.gz", "quality_metric":{ "Sequence length":"35-150", "principals_allowed":{ "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ], "view":[ "award.b0b9c607-f8b4-4f02-93f4-9895b461334b", "group.admin", "group.read-only-admin", "lab.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "remoteuser.EMBED", "remoteuser.INDEXER" ] }, "Total Sequences":905396386, "overall_quality_status":"PASS", "@id":"/quality-metrics-fastqc/fd4ce90a-b78b-4cb3-81ad-75be415f9b35/", "uuid":"fd4ce90a-b78b-4cb3-81ad-75be415f9b35", "url":"https://s3.amazonaws.com/elasticbeanstalk-fourfront-webdev-wfoutput/4DNFIDA6Q5J4/fastqc_report.html", "@type":[ "QualityMetricFastqc", "QualityMetric", "Item" ], "display_title":"QualityMetricFastqc from 2019-08-13" } } ], "type":"input" }, "meta":{ "global":true, "in_path":true, "type":"data file" } }, { "name":"reference", "source":[ { "name":"reference", "for_file":"/files-reference/4DNFIYU3FC57/" } ], "run_data":{ "meta":[ { "workflow_argument_name":"reference", "ordinal":1, "dimension":"0" } ], "file":[ { "experiments":[ ], "accession":"4DNFIYU3FC57", "file_format":{ "file_format":"bwt", "@id":"/file-formats/bwt/", "uuid":"813b0001-5f3f-4e28-9203-4cdf261e19c4", "@type":[ "FileFormat", "Item" ], "principals_allowed":{ "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ], "view":[ "award.b0b9c607-f8b4-4f02-93f4-9895b461334b", "group.admin", "group.read-only-admin", "lab.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "remoteuser.EMBED", "remoteuser.INDEXER" ] }, "display_title":"bwt" }, "@id":"/files-reference/4DNFIYU3FC57/", "uuid":"b24ed5ed-a037-48a0-a938-3fecfb90d0cf", "description":"hg38 bwa genome index for CGAP, untarred, uncompressed", "href":"/files-reference/4DNFIYU3FC57/@@download/4DNFIYU3FC57.bwt", "status":"uploaded", "file_size":3217347004, "@type":[ "FileReference", "File", "Item" ], "display_title":"4DNFIYU3FC57.bwt" } ], "type":"input" }, "meta":{ "global":true, "in_path":true, "type":"reference file" } } ], "outputs":[ { "target":[ { "name":"raw_bam" }, { "name":"input_bam", "for_file":"/files-processed/4DNFIIZ7524H/", "step":"/workflow-runs-awsem/2a1b37e8-eb19-4a35-bb47-fdff61c54ed2/" } ], "name":"raw_bam", "run_data":{ "meta":[ { "format":"/file-formats/bam/", "type":"Output processed file", "upload_key":"c09410af-63f5-4a87-b59f-d7c5a7d3b413/4DNFIIZ7524H.bam" } ], "file":[ { "accession":"4DNFIIZ7524H", "href":"/files-processed/4DNFIIZ7524H/@@download/4DNFIIZ7524H.bam", "uuid":"c09410af-63f5-4a87-b59f-d7c5a7d3b413", "file_size":182498029884, "status":"uploaded", "experiment_sets":[ ], "file_type":"intermediate file", "file_format":{ "file_format":"bam", "@id":"/file-formats/bam/", "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "@type":[ "FileFormat", "Item" ], "display_title":"bam" }, "@id":"/files-processed/4DNFIIZ7524H/", "experiments":[ ], "description":"Intermediate alingnment file", "@type":[ "FileProcessed", "File", "Item" ], "display_title":"4DNFIIZ7524H.bam", "quality_metric":{ "@id":"/quality-metrics-bamcheck/41c6b276-2a6f-4a6c-940c-53aee38fe377/", "@type":[ "QualityMetricBamcheck", "QualityMetric", "Item" ], "display_title":"QualityMetricBamcheck from 2019-08-13", "principals_allowed":{ "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ], "view":[ "award.b0b9c607-f8b4-4f02-93f4-9895b461334b", "group.admin", "group.read-only-admin", "lab.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "remoteuser.EMBED", "remoteuser.INDEXER" ] }, "uuid":"41c6b276-2a6f-4a6c-940c-53aee38fe377" } } ], "type":"input" }, "meta":{ "global":true, "type":"data file", "in_path":true } } ], "meta":{ "run_status":"complete", "date_created":"2019-08-13T00:02:11.315340+00:00", "@id":"/workflow-runs-awsem/d353e726-2a47-4e93-b1f4-cfa7037ee3bc/", "analysis_step_types":[ "processing" ], "status":"in review by lab", "@type":[ "WorkflowRunAwsem", "WorkflowRun", "Item" ], "display_title":"workflow_bwa-mem_no_unzip-check v9 run 2019-08-13 00:02:11.204037", "workflow":{ "accession":"4DNWFAO6TH4V", "@id":"/workflows/9e094699-561b-4396-8d6a-ffc45f98c5e1/", "experiment_types":[ ], "steps":[ { "outputs":[ { "target":[ { "name":"raw_bam", "step":"integrity-check" } ], "meta":{ "global":true, "file_format":"bam", "type":"data file", "cardinality":"single" }, "name":"raw_bam" } ], "inputs":[ { "meta":{ "global":true, "file_format":"c13d06cf-218e-4f61-aaf0-91f226248b2c", "type":"data file", "cardinality":"single" }, "source":[ { "name":"fastq_R1" } ], "name":"fastq_R1" }, { "meta":{ "global":true, "file_format":"c13d06cf-218e-4f61-aaf0-91f226248b2c", "type":"data file", "cardinality":"single" }, "source":[ { "name":"fastq_R2" } ], "name":"fastq_R2" }, { "meta":{ "global":true, "file_format":"813b0001-5f3f-4e28-9203-4cdf261e19c4", "type":"reference file", "cardinality":"single" }, "source":[ { "name":"reference" } ], "name":"reference" }, { "meta":{ "global":true, "type":"parameter", "cardinality":"single" }, "source":[ { "name":"nthreads" } ], "name":"nthreads" } ], "name":"bwa-mem", "meta":{ "analysis_step_types":[ "Align paired-end reads to reference genome" ], "software_used":[ "42adeb1b-c46c-4ba8-b191-56036ddcd544" ] } }, { "outputs":[ { "target":[ { "name":"raw_bam-check" } ], "meta":{ "global":true, "type":"QC", "cardinality":"single" }, "name":"raw_bam-check" } ], "inputs":[ { "meta":{ "global":false, "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "type":"data file", "cardinality":"single" }, "source":[ { "name":"raw_bam", "step":"bwa-mem" } ], "name":"raw_bam" }, { "meta":{ "global":true, "type":"parameter", "cardinality":"single" }, "source":[ { "name":"count" } ], "name":"count" } ], "name":"integrity-check", "meta":{ "analysis_step_types":[ "Check integrity of output file" ], "software_used":[ "3f2d3b0e-0365-4212-9468-c16ad9531c4d" ] } } ], "uuid":"9e094699-561b-4396-8d6a-ffc45f98c5e1", "category":[ "processing" ], "@type":[ "Workflow", "Item" ], "display_title":"Paired-end reads alignment to reference plus output integrity-check - 4DNWFAO6TH4V" } } }, { "name":"/workflow-runs-awsem/2a1b37e8-eb19-4a35-bb47-fdff61c54ed2/", "inputs":[ { "name":"input_bam", "source":[ { "name":"raw_bam", "workflow":"/workflows/9e094699-561b-4396-8d6a-ffc45f98c5e1/", "for_file":"/files-processed/4DNFIIZ7524H/", "step":"/workflow-runs-awsem/d353e726-2a47-4e93-b1f4-cfa7037ee3bc/" } ], "run_data":{ "meta":[ { "workflow_argument_name":"input_bam", "ordinal":1, "dimension":"0" } ], "file":[ { "accession":"4DNFIIZ7524H", "href":"/files-processed/4DNFIIZ7524H/@@download/4DNFIIZ7524H.bam", "uuid":"c09410af-63f5-4a87-b59f-d7c5a7d3b413", "file_size":182498029884, "status":"uploaded", "experiment_sets":[ ], "file_type":"intermediate file", "file_format":{ "file_format":"bam", "@id":"/file-formats/bam/", "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "@type":[ "FileFormat", "Item" ], "display_title":"bam" }, "@id":"/files-processed/4DNFIIZ7524H/", "experiments":[ ], "description":"Intermediate alingnment file", "@type":[ "FileProcessed", "File", "Item" ], "display_title":"4DNFIIZ7524H.bam", "quality_metric":{ "@id":"/quality-metrics-bamcheck/41c6b276-2a6f-4a6c-940c-53aee38fe377/", "@type":[ "QualityMetricBamcheck", "QualityMetric", "Item" ], "display_title":"QualityMetricBamcheck from 2019-08-13", "principals_allowed":{ "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ], "view":[ "award.b0b9c607-f8b4-4f02-93f4-9895b461334b", "group.admin", "group.read-only-admin", "lab.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "remoteuser.EMBED", "remoteuser.INDEXER" ] }, "uuid":"41c6b276-2a6f-4a6c-940c-53aee38fe377" } } ], "type":"input" }, "meta":{ "global":true, "in_path":true, "type":"data file" } } ], "outputs":[ { "target":[ { "name":"bam_w_readgroups" }, { "name":"input_bam", "for_file":"/files-processed/4DNFIVSKSCE4/", "step":"/workflow-runs-awsem/1079f3d1-0e12-4414-9490-28e0c46013f8/" } ], "name":"bam_w_readgroups", "run_data":{ "meta":[ { "format":"/file-formats/bam/", "type":"Output processed file", "upload_key":"b735205c-a7b9-4110-a678-b43be35e6191/4DNFIVSKSCE4.bam" } ], "file":[ { "accession":"4DNFIVSKSCE4", "href":"/files-processed/4DNFIVSKSCE4/@@download/4DNFIVSKSCE4.bam", "uuid":"b735205c-a7b9-4110-a678-b43be35e6191", "file_size":188619928471, "status":"uploaded", "experiment_sets":[ ], "file_type":"intermediate file", "file_format":{ "file_format":"bam", "@id":"/file-formats/bam/", "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "@type":[ "FileFormat", "Item" ], "display_title":"bam" }, "@id":"/files-processed/4DNFIVSKSCE4/", "experiments":[ ], "description":"Intermediate alingnment file", "@type":[ "FileProcessed", "File", "Item" ], "display_title":"4DNFIVSKSCE4.bam", "quality_metric":{ "@id":"/quality-metrics-bamcheck/4039970b-7f30-4796-925a-774140eac371/", "@type":[ "QualityMetricBamcheck", "QualityMetric", "Item" ], "display_title":"QualityMetricBamcheck from 2019-08-13", "principals_allowed":{ "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ], "view":[ "award.b0b9c607-f8b4-4f02-93f4-9895b461334b", "group.admin", "group.read-only-admin", "lab.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "remoteuser.EMBED", "remoteuser.INDEXER" ] }, "uuid":"4039970b-7f30-4796-925a-774140eac371" } } ], "type":"input" }, "meta":{ "global":true, "type":"data file", "in_path":true } } ], "meta":{ "run_status":"complete", "date_created":"2019-08-13T11:01:10.137893+00:00", "@id":"/workflow-runs-awsem/2a1b37e8-eb19-4a35-bb47-fdff61c54ed2/", "analysis_step_types":[ "processing" ], "status":"in review by lab", "@type":[ "WorkflowRunAwsem", "WorkflowRun", "Item" ], "display_title":"workflow_add-readgroups-check v9 run 2019-08-13 11:01:10.091750", "workflow":{ "accession":"4DNWF3GB8UI2", "@id":"/workflows/548e63a4-1936-4f68-8e8d-8e4658767911/", "experiment_types":[ ], "steps":[ { "name":"add-readgroups", "inputs":[ { "name":"input_bam", "source":[ { "name":"input_bam" } ], "meta":{ "global":true, "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "cardinality":"single", "type":"data file" } }, { "name":"sample_name", "source":[ { "name":"sample_name" } ], "meta":{ "global":true, "cardinality":"single", "type":"parameter" } }, { "name":"nthreads", "source":[ { "name":"nthreads" } ], "meta":{ "global":true, "cardinality":"single", "type":"parameter" } } ], "outputs":[ { "target":[ { "name":"bam_w_readgroups", "step":"integrity-check" } ], "name":"bam_w_readgroups", "meta":{ "global":true, "file_format":"bam", "cardinality":"single", "type":"data file" } } ], "meta":{ "analysis_step_types":[ "Add read groups to bam input file" ], "software_used":[ "d7ac4c75-e133-4a8e-a19e-b7e87873cc16" ] } }, { "name":"integrity-check", "inputs":[ { "name":"bam_w_readgroups", "source":[ { "name":"bam_w_readgroups", "step":"add-readgroups" } ], "meta":{ "global":false, "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "cardinality":"single", "type":"data file" } }, { "name":"count", "source":[ { "name":"count" } ], "meta":{ "global":true, "cardinality":"single", "type":"parameter" } } ], "outputs":[ { "target":[ { "name":"bam_w_readgroups-check" } ], "name":"bam_w_readgroups-check", "meta":{ "global":true, "cardinality":"single", "type":"QC" } } ], "meta":{ "analysis_step_types":[ "Check integrity of output file" ], "software_used":[ "3f2d3b0e-0365-4212-9468-c16ad9531c4d" ] } } ], "uuid":"548e63a4-1936-4f68-8e8d-8e4658767911", "category":[ "processing" ], "@type":[ "Workflow", "Item" ], "display_title":"Add read groups plus output integrity-check - 4DNWF3GB8UI2" } } }, { "name":"/workflow-runs-awsem/1079f3d1-0e12-4414-9490-28e0c46013f8/", "inputs":[ { "name":"input_bam", "source":[ { "name":"bam_w_readgroups", "workflow":"/workflows/548e63a4-1936-4f68-8e8d-8e4658767911/", "for_file":"/files-processed/4DNFIVSKSCE4/", "step":"/workflow-runs-awsem/2a1b37e8-eb19-4a35-bb47-fdff61c54ed2/" } ], "run_data":{ "meta":[ { "workflow_argument_name":"input_bam", "ordinal":1, "dimension":"0" } ], "file":[ { "accession":"4DNFIVSKSCE4", "href":"/files-processed/4DNFIVSKSCE4/@@download/4DNFIVSKSCE4.bam", "uuid":"b735205c-a7b9-4110-a678-b43be35e6191", "file_size":188619928471, "status":"uploaded", "experiment_sets":[ ], "file_type":"intermediate file", "file_format":{ "file_format":"bam", "@id":"/file-formats/bam/", "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "@type":[ "FileFormat", "Item" ], "display_title":"bam" }, "@id":"/files-processed/4DNFIVSKSCE4/", "experiments":[ ], "description":"Intermediate alingnment file", "@type":[ "FileProcessed", "File", "Item" ], "display_title":"4DNFIVSKSCE4.bam", "quality_metric":{ "@id":"/quality-metrics-bamcheck/4039970b-7f30-4796-925a-774140eac371/", "@type":[ "QualityMetricBamcheck", "QualityMetric", "Item" ], "display_title":"QualityMetricBamcheck from 2019-08-13", "principals_allowed":{ "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ], "view":[ "award.b0b9c607-f8b4-4f02-93f4-9895b461334b", "group.admin", "group.read-only-admin", "lab.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "remoteuser.EMBED", "remoteuser.INDEXER" ] }, "uuid":"4039970b-7f30-4796-925a-774140eac371" } } ], "type":"input" }, "meta":{ "global":true, "in_path":true, "type":"data file" } } ], "outputs":[ { "target":[ { "name":"dupmarked_bam" }, { "name":"input_bam", "for_file":"/files-processed/4DNFINI1BY5G/", "step":"/workflow-runs-awsem/5a5a23fe-f7aa-494b-94ea-c062cc5289ac/" }, { "name":"input_bam", "for_file":"/files-processed/4DNFINI1BY5G/", "step":"/workflow-runs-awsem/b0cec4b1-7645-444c-a8a4-e99ab445bb69/" }, { "name":"input_bam", "for_file":"/files-processed/4DNFINI1BY5G/", "step":"/workflow-runs-awsem/8792763c-ea36-495e-ae97-a023c55ece5f/" }, { "name":"input_bam", "for_file":"/files-processed/4DNFINI1BY5G/", "step":"/workflow-runs-awsem/5a5a23fe-f7aa-494b-94ea-c062cc5289ac/" }, { "name":"input_bam", "for_file":"/files-processed/4DNFINI1BY5G/", "step":"/workflow-runs-awsem/b0cec4b1-7645-444c-a8a4-e99ab445bb69/" }, { "name":"input_bam", "for_file":"/files-processed/4DNFINI1BY5G/", "step":"/workflow-runs-awsem/8792763c-ea36-495e-ae97-a023c55ece5f/" } ], "name":"dupmarked_bam", "run_data":{ "meta":[ { "format":"/file-formats/bam/", "type":"Output processed file", "upload_key":"76d334a0-aa3f-4f3b-9c08-41e4b70fca0c/4DNFINI1BY5G.bam" } ], "file":[ { "accession":"4DNFINI1BY5G", "href":"/files-processed/4DNFINI1BY5G/@@download/4DNFINI1BY5G.bam", "uuid":"76d334a0-aa3f-4f3b-9c08-41e4b70fca0c", "file_size":184529007374, "status":"uploaded", "experiment_sets":[ ], "file_type":"intermediate file", "file_format":{ "file_format":"bam", "@id":"/file-formats/bam/", "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "@type":[ "FileFormat", "Item" ], "display_title":"bam" }, "@id":"/files-processed/4DNFINI1BY5G/", "experiments":[ ], "description":"Intermediate alingnment file", "@type":[ "FileProcessed", "File", "Item" ], "display_title":"4DNFINI1BY5G.bam", "quality_metric":{ "@id":"/quality-metrics-bamcheck/a8d27ec1-b35e-48f5-8868-7dd339e7ce38/", "@type":[ "QualityMetricBamcheck", "QualityMetric", "Item" ], "display_title":"QualityMetricBamcheck from 2019-08-14", "principals_allowed":{ "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ], "view":[ "award.b0b9c607-f8b4-4f02-93f4-9895b461334b", "group.admin", "group.read-only-admin", "lab.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "remoteuser.EMBED", "remoteuser.INDEXER" ] }, "uuid":"a8d27ec1-b35e-48f5-8868-7dd339e7ce38" } } ], "type":"input" }, "meta":{ "global":true, "type":"data file", "in_path":true } }, { "target":[ { "name":"duplicate_metrics" } ], "name":"duplicate_metrics", "run_data":{ "meta":[ { "format":"/file-formats/txt/", "type":"Output processed file", "upload_key":"df26d9e5-1196-4d8f-a6ca-18c7d5a89572/4DNFIRC7WHUC.txt" } ], "file":[ { "experiments":[ ], "accession":"4DNFIRC7WHUC", "file_format":{ "file_format":"txt", "@id":"/file-formats/txt/", "uuid":"0cd4e777-a596-4927-95c8-b07716121aa3", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "@type":[ "FileFormat", "Item" ], "display_title":"txt" }, "@id":"/files-processed/4DNFIRC7WHUC/", "uuid":"df26d9e5-1196-4d8f-a6ca-18c7d5a89572", "href":"/files-processed/4DNFIRC7WHUC/@@download/4DNFIRC7WHUC.txt", "status":"uploaded", "file_size":7999, "@type":[ "FileProcessed", "File", "Item" ], "display_title":"4DNFIRC7WHUC.txt", "experiment_sets":[ ] } ], "type":"input" }, "meta":{ "global":true, "type":"data file", "in_path":false } } ], "meta":{ "run_status":"complete", "date_created":"2019-08-14T01:01:30.239423+00:00", "@id":"/workflow-runs-awsem/1079f3d1-0e12-4414-9490-28e0c46013f8/", "analysis_step_types":[ "processing" ], "status":"in review by lab", "@type":[ "WorkflowRunAwsem", "WorkflowRun", "Item" ], "display_title":"workflow_picard-MarkDuplicates-check v9 run 2019-08-14 01:01:30.181132", "workflow":{ "accession":"4DNWFR5HG6J1", "@id":"/workflows/beb2b340-94ee-4afe-b4e3-66caaf063397/", "experiment_types":[ ], "steps":[ { "outputs":[ { "target":[ { "name":"dupmarked_bam", "step":"integrity-check" } ], "name":"dupmarked_bam", "meta":{ "global":true, "file_format":"bam", "type":"data file", "cardinality":"single" } }, { "target":[ { "name":"duplicate_metrics" } ], "name":"duplicate_metrics", "meta":{ "global":true, "file_format":"txt", "type":"data file", "cardinality":"single" } } ], "meta":{ "analysis_step_types":[ "Mark duplicates in bam input file" ], "software_used":[ "586cef39-6505-4bf6-920a-4b26a500d210" ] }, "name":"MarkDuplicates", "inputs":[ { "name":"input_bam", "source":[ { "name":"input_bam" } ], "meta":{ "global":true, "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "type":"data file", "cardinality":"single" } }, { "name":"xmx", "source":[ { "name":"xmx" } ], "meta":{ "global":true, "type":"parameter", "cardinality":"single" } }, { "name":"xms", "source":[ { "name":"xms" } ], "meta":{ "global":true, "type":"parameter", "cardinality":"single" } }, { "name":"max_records_in_ram", "source":[ { "name":"max_records_in_ram" } ], "meta":{ "global":true, "type":"parameter", "cardinality":"single" } }, { "name":"duplicate_pixel_distance", "source":[ { "name":"duplicate_pixel_distance" } ], "meta":{ "global":true, "type":"parameter", "cardinality":"single" } } ] }, { "outputs":[ { "target":[ { "name":"dupmarked_bam-check" } ], "name":"dupmarked_bam-check", "meta":{ "global":true, "type":"report", "cardinality":"single" } } ], "meta":{ "analysis_step_types":[ "Check integrity of output file" ], "software_used":[ "3f2d3b0e-0365-4212-9468-c16ad9531c4d" ] }, "name":"integrity-check", "inputs":[ { "name":"dupmarked_bam", "source":[ { "name":"dupmarked_bam", "step":"MarkDuplicates" } ], "meta":{ "global":false, "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "type":"data file", "cardinality":"single" } }, { "name":"count", "source":[ { "name":"count" } ], "meta":{ "global":true, "type":"parameter", "cardinality":"single" } } ] } ], "uuid":"beb2b340-94ee-4afe-b4e3-66caaf063397", "category":[ "processing" ], "@type":[ "Workflow", "Item" ], "display_title":"Mark duplicates plus output integrity-check - 4DNWFR5HG6J1" } } }, { "name":"/workflow-runs-awsem/8792763c-ea36-495e-ae97-a023c55ece5f/", "inputs":[ { "name":"input_bam", "source":[ { "name":"dupmarked_bam", "workflow":"/workflows/beb2b340-94ee-4afe-b4e3-66caaf063397/", "for_file":"/files-processed/4DNFINI1BY5G/", "step":"/workflow-runs-awsem/1079f3d1-0e12-4414-9490-28e0c46013f8/" } ], "run_data":{ "meta":[ { "workflow_argument_name":"input_bam", "ordinal":1, "dimension":"0" } ], "file":[ { "accession":"4DNFINI1BY5G", "href":"/files-processed/4DNFINI1BY5G/@@download/4DNFINI1BY5G.bam", "uuid":"76d334a0-aa3f-4f3b-9c08-41e4b70fca0c", "file_size":184529007374, "status":"uploaded", "experiment_sets":[ ], "file_type":"intermediate file", "file_format":{ "file_format":"bam", "@id":"/file-formats/bam/", "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "@type":[ "FileFormat", "Item" ], "display_title":"bam" }, "@id":"/files-processed/4DNFINI1BY5G/", "experiments":[ ], "description":"Intermediate alingnment file", "@type":[ "FileProcessed", "File", "Item" ], "display_title":"4DNFINI1BY5G.bam", "quality_metric":{ "@id":"/quality-metrics-bamcheck/a8d27ec1-b35e-48f5-8868-7dd339e7ce38/", "@type":[ "QualityMetricBamcheck", "QualityMetric", "Item" ], "display_title":"QualityMetricBamcheck from 2019-08-14", "principals_allowed":{ "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ], "view":[ "award.b0b9c607-f8b4-4f02-93f4-9895b461334b", "group.admin", "group.read-only-admin", "lab.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "remoteuser.EMBED", "remoteuser.INDEXER" ] }, "uuid":"a8d27ec1-b35e-48f5-8868-7dd339e7ce38" } } ], "type":"input" }, "meta":{ "global":true, "in_path":true, "type":"data file" } } ], "outputs":[ { "target":[ { "name":"sorted_bam" }, { "name":"input_bam", "for_file":"/files-processed/4DNFI5SMG9FV/", "step":"/workflow-runs-awsem/c61bc2d6-5f3a-4100-904f-601f37be2bff/" }, { "name":"input_bam", "for_file":"/files-processed/4DNFI5SMG9FV/", "step":"/workflow-runs-awsem/818236d0-71fe-4116-92b7-d1fb57ae6ef9/" } ], "name":"sorted_bam", "run_data":{ "meta":[ { "format":"/file-formats/bam/", "type":"Output processed file", "upload_key":"64434c59-0511-4d0c-8812-047a8f1f080a/4DNFI5SMG9FV.bam" } ], "file":[ { "accession":"4DNFI5SMG9FV", "href":"/files-processed/4DNFI5SMG9FV/@@download/4DNFI5SMG9FV.bam", "uuid":"64434c59-0511-4d0c-8812-047a8f1f080a", "file_size":106901046325, "status":"uploaded", "experiment_sets":[ ], "file_type":"intermediate file", "file_format":{ "file_format":"bam", "@id":"/file-formats/bam/", "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "@type":[ "FileFormat", "Item" ], "display_title":"bam" }, "@id":"/files-processed/4DNFI5SMG9FV/", "experiments":[ ], "description":"Intermediate alingnment file", "@type":[ "FileProcessed", "File", "Item" ], "display_title":"4DNFI5SMG9FV.bam", "quality_metric":{ "@id":"/quality-metrics-bamcheck/a5718951-9a7b-46d9-baf3-745dbb383b9d/", "@type":[ "QualityMetricBamcheck", "QualityMetric", "Item" ], "display_title":"QualityMetricBamcheck from 2019-08-14", "principals_allowed":{ "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ], "view":[ "award.b0b9c607-f8b4-4f02-93f4-9895b461334b", "group.admin", "group.read-only-admin", "lab.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "remoteuser.EMBED", "remoteuser.INDEXER" ] }, "uuid":"a5718951-9a7b-46d9-baf3-745dbb383b9d" } } ], "type":"input" }, "meta":{ "global":true, "type":"data file", "in_path":true } } ], "meta":{ "run_status":"complete", "date_created":"2019-08-14T13:14:45.409621+00:00", "@id":"/workflow-runs-awsem/8792763c-ea36-495e-ae97-a023c55ece5f/", "analysis_step_types":[ "processing" ], "status":"in review by lab", "@type":[ "WorkflowRunAwsem", "WorkflowRun", "Item" ], "display_title":"workflow_sort-bam-check v9 run 2019-08-14 13:14:45.360190", "workflow":{ "accession":"4DNWFKW3RD8Q", "@id":"/workflows/560f5194-cd3a-4799-9b1a-6a2d2c371c89/", "experiment_types":[ ], "steps":[ { "name":"sort", "inputs":[ { "name":"input_bam", "source":[ { "name":"input_bam" } ], "meta":{ "global":true, "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "cardinality":"single", "type":"data file" } }, { "name":"max_memory", "source":[ { "name":"max_memory" } ], "meta":{ "global":true, "cardinality":"single", "type":"parameter" } }, { "name":"nthreads", "source":[ { "name":"nthreads" } ], "meta":{ "global":true, "cardinality":"single", "type":"parameter" } } ], "outputs":[ { "target":[ { "name":"sorted_bam", "step":"integrity-check" } ], "name":"sorted_bam", "meta":{ "global":true, "file_format":"bam", "cardinality":"single", "type":"data file" } } ], "meta":{ "analysis_step_types":[ "Sort bam input file" ], "software_used":[ "3f2d3b0e-0365-4212-9468-c16ad9531c4d" ] } }, { "name":"integrity-check", "inputs":[ { "name":"sorted_bam", "source":[ { "name":"sorted_bam", "step":"sort" } ], "meta":{ "global":false, "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "cardinality":"single", "type":"data file" } }, { "name":"count", "source":[ { "name":"count" } ], "meta":{ "global":true, "cardinality":"single", "type":"parameter" } } ], "outputs":[ { "target":[ { "name":"sorted_bam-check" } ], "name":"sorted_bam-check", "meta":{ "global":true, "cardinality":"single", "type":"QC" } } ], "meta":{ "analysis_step_types":[ "Check integrity of output file" ], "software_used":[ "3f2d3b0e-0365-4212-9468-c16ad9531c4d" ] } } ], "uuid":"560f5194-cd3a-4799-9b1a-6a2d2c371c89", "category":[ "processing" ], "@type":[ "Workflow", "Item" ], "display_title":"Sort bam file plus output integrity-check - 4DNWFKW3RD8Q" } } }, { "name":"/workflow-runs-awsem/c61bc2d6-5f3a-4100-904f-601f37be2bff/", "inputs":[ { "name":"input_bam", "source":[ { "name":"sorted_bam", "workflow":"/workflows/560f5194-cd3a-4799-9b1a-6a2d2c371c89/", "for_file":"/files-processed/4DNFI5SMG9FV/", "step":"/workflow-runs-awsem/8792763c-ea36-495e-ae97-a023c55ece5f/" } ], "run_data":{ "meta":[ { "workflow_argument_name":"input_bam", "ordinal":1, "dimension":"0" } ], "file":[ { "accession":"4DNFI5SMG9FV", "href":"/files-processed/4DNFI5SMG9FV/@@download/4DNFI5SMG9FV.bam", "uuid":"64434c59-0511-4d0c-8812-047a8f1f080a", "file_size":106901046325, "status":"uploaded", "experiment_sets":[ ], "file_type":"intermediate file", "file_format":{ "file_format":"bam", "@id":"/file-formats/bam/", "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "@type":[ "FileFormat", "Item" ], "display_title":"bam" }, "@id":"/files-processed/4DNFI5SMG9FV/", "experiments":[ ], "description":"Intermediate alingnment file", "@type":[ "FileProcessed", "File", "Item" ], "display_title":"4DNFI5SMG9FV.bam", "quality_metric":{ "@id":"/quality-metrics-bamcheck/a5718951-9a7b-46d9-baf3-745dbb383b9d/", "@type":[ "QualityMetricBamcheck", "QualityMetric", "Item" ], "display_title":"QualityMetricBamcheck from 2019-08-14", "principals_allowed":{ "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ], "view":[ "award.b0b9c607-f8b4-4f02-93f4-9895b461334b", "group.admin", "group.read-only-admin", "lab.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "remoteuser.EMBED", "remoteuser.INDEXER" ] }, "uuid":"a5718951-9a7b-46d9-baf3-745dbb383b9d" } } ], "type":"input" }, "meta":{ "global":true, "in_path":true, "type":"data file" } }, { "name":"known-sites-indels", "source":[ { "name":"known-sites-indels", "for_file":"/files-reference/4DNFIBN3576F/" } ], "run_data":{ "meta":[ { "workflow_argument_name":"known-sites-indels", "ordinal":1, "dimension":"0" } ], "file":[ { "experiments":[ ], "accession":"4DNFIBN3576F", "file_format":{ "file_format":"vcf", "@id":"/file-formats/vcf/", "uuid":"fcc2647d-301b-4888-8d9d-83ea4270309c", "@type":[ "FileFormat", "Item" ], "principals_allowed":{ "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ], "view":[ "award.b0b9c607-f8b4-4f02-93f4-9895b461334b", "group.admin", "group.read-only-admin", "lab.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "remoteuser.EMBED", "remoteuser.INDEXER" ] }, "display_title":"vcf" }, "@id":"/files-reference/4DNFIBN3576F/", "uuid":"55ac5044-f927-4df7-afa2-bf713764ee57", "description":"hg38 Mills_and_1000G_gold_standard_indels", "href":"/files-reference/4DNFIBN3576F/@@download/4DNFIBN3576F.vcf", "status":"uploaded", "file_size":90155308, "@type":[ "FileReference", "File", "Item" ], "display_title":"4DNFIBN3576F.vcf" } ], "type":"input" }, "meta":{ "global":true, "in_path":true, "type":"reference file" } }, { "name":"known-sites-snp", "source":[ { "name":"known-sites-snp", "for_file":"/files-reference/4DNFI2RDOLUQ/" } ], "run_data":{ "meta":[ { "workflow_argument_name":"known-sites-snp", "ordinal":1, "dimension":"0" } ], "file":[ { "experiments":[ ], "accession":"4DNFI2RDOLUQ", "file_format":{ "file_format":"vcf_gz", "@id":"/file-formats/vcf_gz/", "uuid":"1b8f525f-aecb-4211-9ae5-a2c998b05599", "@type":[ "FileFormat", "Item" ], "principals_allowed":{ "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ], "view":[ "award.b0b9c607-f8b4-4f02-93f4-9895b461334b", "group.admin", "group.read-only-admin", "lab.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "remoteuser.EMBED", "remoteuser.INDEXER" ] }, "display_title":"vcf_gz" }, "@id":"/files-reference/4DNFI2RDOLUQ/", "uuid":"8ed35691-0af4-467a-adbc-81eb088549f0", "description":"hg38 dbsnp_b151", "href":"/files-reference/4DNFI2RDOLUQ/@@download/4DNFI2RDOLUQ.vcf.gz", "status":"uploaded", "file_size":1595848625, "@type":[ "FileReference", "File", "Item" ], "display_title":"4DNFI2RDOLUQ.vcf.gz" } ], "type":"input" }, "meta":{ "global":true, "in_path":true, "type":"reference file" } }, { "name":"reference", "source":[ { "name":"reference", "for_file":"/files-reference/4DNFIBH13WES/" } ], "run_data":{ "meta":[ { "workflow_argument_name":"reference", "ordinal":1, "dimension":"0" } ], "file":[ { "experiments":[ ], "accession":"4DNFIBH13WES", "file_format":{ "file_format":"fa", "@id":"/file-formats/fa/", "uuid":"5ced774b-a73e-4d1b-8186-d7fbbde7a3c2", "principals_allowed":{ "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ], "view":[ "award.b0b9c607-f8b4-4f02-93f4-9895b461334b", "group.admin", "group.read-only-admin", "lab.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "remoteuser.EMBED", "remoteuser.INDEXER" ] }, "@type":[ "FileFormat", "Item" ], "display_title":"fa" }, "@id":"/files-reference/4DNFIBH13WES/", "uuid":"1936f246-22e1-45dc-bb5c-9cfd55537fe7", "description":"hg38 full reference fasta plus decoy for CGAP", "href":"/files-reference/4DNFIBH13WES/@@download/4DNFIBH13WES.fa", "status":"released", "file_size":3263683042, "@type":[ "FileReference", "File", "Item" ], "display_title":"4DNFIBH13WES.fa" } ], "type":"input" }, "meta":{ "global":true, "in_path":true, "type":"reference file" } } ], "outputs":[ { "target":[ { "name":"recalibration_report" }, { "name":"recalibration_report", "for_file":"/files-processed/4DNFIKHIZTLT/", "step":"/workflow-runs-awsem/818236d0-71fe-4116-92b7-d1fb57ae6ef9/" } ], "name":"recalibration_report", "run_data":{ "meta":[ { "format":"/file-formats/txt/", "type":"Output processed file", "upload_key":"bbb9297a-1194-4d3e-b444-5e8b95a455bf/4DNFIKHIZTLT.txt" } ], "file":[ { "accession":"4DNFIKHIZTLT", "href":"/files-processed/4DNFIKHIZTLT/@@download/4DNFIKHIZTLT.txt", "uuid":"bbb9297a-1194-4d3e-b444-5e8b95a455bf", "file_size":474558, "status":"uploaded", "experiment_sets":[ ], "file_type":"intermediate file", "file_format":{ "file_format":"txt", "@id":"/file-formats/txt/", "uuid":"0cd4e777-a596-4927-95c8-b07716121aa3", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "@type":[ "FileFormat", "Item" ], "display_title":"txt" }, "@id":"/files-processed/4DNFIKHIZTLT/", "experiments":[ ], "description":"Intermediate alingnment file", "@type":[ "FileProcessed", "File", "Item" ], "display_title":"4DNFIKHIZTLT.txt" } ], "type":"input" }, "meta":{ "global":true, "type":"data file", "in_path":true } } ], "meta":{ "run_status":"complete", "date_created":"2019-08-14T17:01:24.198817+00:00", "@id":"/workflow-runs-awsem/c61bc2d6-5f3a-4100-904f-601f37be2bff/", "analysis_step_types":[ "processing" ], "status":"in review by lab", "@type":[ "WorkflowRunAwsem", "WorkflowRun", "Item" ], "display_title":"workflow_gatk-BaseRecalibrator v9 run 2019-08-14 17:01:24.113136", "workflow":{ "accession":"4DNWFVI33YB5", "@id":"/workflows/455b3056-64ca-4a9b-b546-294b01c9ca92/", "experiment_types":[ ], "steps":[ { "meta":{ "analysis_step_types":[ "Run gatk BaseRecalibrator" ], "software_used":[ "4ae88fb4-23f2-4939-8852-4644069d14d9" ] }, "inputs":[ { "meta":{ "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "global":true, "type":"data file", "cardinality":"single" }, "source":[ { "name":"input_bam" } ], "name":"input_bam" }, { "meta":{ "file_format":"5ced774b-a73e-4d1b-8186-d7fbbde7a3c2", "global":true, "type":"reference file", "cardinality":"single" }, "source":[ { "name":"reference" } ], "name":"reference" }, { "meta":{ "file_format":"1b8f525f-aecb-4211-9ae5-a2c998b05599", "global":true, "type":"reference file", "cardinality":"single" }, "source":[ { "name":"known-sites-snp" } ], "name":"known-sites-snp" }, { "meta":{ "file_format":"fcc2647d-301b-4888-8d9d-83ea4270309c", "global":true, "type":"reference file", "cardinality":"single" }, "source":[ { "name":"known-sites-indels" } ], "name":"known-sites-indels" } ], "outputs":[ { "target":[ { "name":"recalibration_report" } ], "meta":{ "file_format":"txt", "global":true, "type":"data file", "cardinality":"single" }, "name":"recalibration_report" } ], "name":"BaseRecalibrator" } ], "uuid":"455b3056-64ca-4a9b-b546-294b01c9ca92", "category":[ "processing" ], "@type":[ "Workflow", "Item" ], "display_title":"Run gatk BaseRecalibrator - 4DNWFVI33YB5" } } }, { "name":"/workflow-runs-awsem/818236d0-71fe-4116-92b7-d1fb57ae6ef9/", "inputs":[ { "name":"input_bam", "source":[ { "name":"sorted_bam", "workflow":"/workflows/560f5194-cd3a-4799-9b1a-6a2d2c371c89/", "for_file":"/files-processed/4DNFI5SMG9FV/", "step":"/workflow-runs-awsem/8792763c-ea36-495e-ae97-a023c55ece5f/" } ], "run_data":{ "meta":[ { "workflow_argument_name":"input_bam", "ordinal":1, "dimension":"0" } ], "file":[ { "accession":"4DNFI5SMG9FV", "href":"/files-processed/4DNFI5SMG9FV/@@download/4DNFI5SMG9FV.bam", "uuid":"64434c59-0511-4d0c-8812-047a8f1f080a", "file_size":106901046325, "status":"uploaded", "experiment_sets":[ ], "file_type":"intermediate file", "file_format":{ "file_format":"bam", "@id":"/file-formats/bam/", "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "@type":[ "FileFormat", "Item" ], "display_title":"bam" }, "@id":"/files-processed/4DNFI5SMG9FV/", "experiments":[ ], "description":"Intermediate alingnment file", "@type":[ "FileProcessed", "File", "Item" ], "display_title":"4DNFI5SMG9FV.bam", "quality_metric":{ "@id":"/quality-metrics-bamcheck/a5718951-9a7b-46d9-baf3-745dbb383b9d/", "@type":[ "QualityMetricBamcheck", "QualityMetric", "Item" ], "display_title":"QualityMetricBamcheck from 2019-08-14", "principals_allowed":{ "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ], "view":[ "award.b0b9c607-f8b4-4f02-93f4-9895b461334b", "group.admin", "group.read-only-admin", "lab.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "remoteuser.EMBED", "remoteuser.INDEXER" ] }, "uuid":"a5718951-9a7b-46d9-baf3-745dbb383b9d" } } ], "type":"input" }, "meta":{ "global":true, "in_path":true, "type":"data file" } }, { "name":"recalibration_report", "source":[ { "name":"recalibration_report", "workflow":"/workflows/455b3056-64ca-4a9b-b546-294b01c9ca92/", "for_file":"/files-processed/4DNFIKHIZTLT/", "step":"/workflow-runs-awsem/c61bc2d6-5f3a-4100-904f-601f37be2bff/" } ], "run_data":{ "meta":[ { "workflow_argument_name":"recalibration_report", "ordinal":1, "dimension":"0" } ], "file":[ { "accession":"4DNFIKHIZTLT", "href":"/files-processed/4DNFIKHIZTLT/@@download/4DNFIKHIZTLT.txt", "uuid":"bbb9297a-1194-4d3e-b444-5e8b95a455bf", "file_size":474558, "status":"uploaded", "experiment_sets":[ ], "file_type":"intermediate file", "file_format":{ "file_format":"txt", "@id":"/file-formats/txt/", "uuid":"0cd4e777-a596-4927-95c8-b07716121aa3", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "@type":[ "FileFormat", "Item" ], "display_title":"txt" }, "@id":"/files-processed/4DNFIKHIZTLT/", "experiments":[ ], "description":"Intermediate alingnment file", "@type":[ "FileProcessed", "File", "Item" ], "display_title":"4DNFIKHIZTLT.txt" } ], "type":"input" }, "meta":{ "global":true, "in_path":true, "type":"data file" } }, { "name":"reference", "source":[ { "name":"reference", "for_file":"/files-reference/4DNFIBH13WES/" } ], "run_data":{ "meta":[ { "workflow_argument_name":"reference", "ordinal":1, "dimension":"0" } ], "file":[ { "experiments":[ ], "accession":"4DNFIBH13WES", "file_format":{ "file_format":"fa", "@id":"/file-formats/fa/", "uuid":"5ced774b-a73e-4d1b-8186-d7fbbde7a3c2", "principals_allowed":{ "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ], "view":[ "award.b0b9c607-f8b4-4f02-93f4-9895b461334b", "group.admin", "group.read-only-admin", "lab.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "remoteuser.EMBED", "remoteuser.INDEXER" ] }, "@type":[ "FileFormat", "Item" ], "display_title":"fa" }, "@id":"/files-reference/4DNFIBH13WES/", "uuid":"1936f246-22e1-45dc-bb5c-9cfd55537fe7", "description":"hg38 full reference fasta plus decoy for CGAP", "href":"/files-reference/4DNFIBH13WES/@@download/4DNFIBH13WES.fa", "status":"released", "file_size":3263683042, "@type":[ "FileReference", "File", "Item" ], "display_title":"4DNFIBH13WES.fa" } ], "type":"input" }, "meta":{ "global":true, "in_path":true, "type":"reference file" } } ], "outputs":[ { "target":[ { "name":"recalibrated_bam" } ], "name":"recalibrated_bam", "run_data":{ "meta":[ { "extra_files":[ { "accession":"4DNFI9WF1Y8W", "file_format":"/file-formats/bai/", "href":"/8a64c5e9-b669-425c-a78a-3177abc9ebd5/@@download/4DNFI9WF1Y8W.bam.bai", "upload_key":"8a64c5e9-b669-425c-a78a-3177abc9ebd5/4DNFI9WF1Y8W.bam.bai", "uuid":"8a64c5e9-b669-425c-a78a-3177abc9ebd5", "status":"uploading", "filename":"4DNFI9WF1Y8W" } ], "secondary_file_formats":[ "/file-formats/bai/" ], "format":"/file-formats/bam/", "type":"Output processed file", "upload_key":"8a64c5e9-b669-425c-a78a-3177abc9ebd5/4DNFI9WF1Y8W.bam" } ], "file":[ { "accession":"4DNFI9WF1Y8W", "href":"/files-processed/4DNFI9WF1Y8W/@@download/4DNFI9WF1Y8W.bam", "uuid":"8a64c5e9-b669-425c-a78a-3177abc9ebd5", "file_size":140552384892, "status":"uploaded", "experiment_sets":[ ], "file_type":"alignments", "file_format":{ "file_format":"bam", "@id":"/file-formats/bam/", "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed":{ "edit":[ "group.admin" ], "view":[ "system.Everyone" ] }, "@type":[ "FileFormat", "Item" ], "display_title":"bam" }, "@id":"/files-processed/4DNFI9WF1Y8W/", "experiments":[ { "experiment_sets":[ { "@id":"/experiment-set-replicates/4DNESNRXSDZB/", "uuid":"e6211c0c-5382-4026-a41a-a442af0163aa" } ], "@id":"/experiments-seq/4DNEXBT1CT94/", "uuid":"cd049338-8856-4a37-b2ca-4c81aaf52903" } ], "description":"processed output from cgap pipeline", "@type":[ "FileProcessed", "File", "Item" ], "display_title":"4DNFI9WF1Y8W.bam", "quality_metric":{ "@type":[ "QualityMetricBamcheck", "QualityMetric", "Item" ], "@id":"/quality-metrics-bamcheck/d320f68b-7a33-485a-a735-55a9c91170e7/", "display_title":"QualityMetricBamcheck from 2019-08-15", "principals_allowed":{ "edit":[ "group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989" ], "view":[ "award.b0b9c607-f8b4-4f02-93f4-9895b461334b", "group.admin", "group.read-only-admin", "lab.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "remoteuser.EMBED", "remoteuser.INDEXER" ] }, "uuid":"d320f68b-7a33-485a-a735-55a9c91170e7" } } ], "type":"input" }, "meta":{ "global":true, "type":"data file", "in_path":true } }, { "target":[ { "name":"recalibrated_bam-check" } ], "name":"recalibrated_bam-check", "run_data":{ "meta":[ { "type":"Output QC file" } ], "file":[ { "accession":null, "@id":"/quality-metrics-bamcheck/d320f68b-7a33-485a-a735-55a9c91170e7/", "uuid":"d320f68b-7a33-485a-a735-55a9c91170e7", "status":"in review by lab", "@type":[ "QualityMetricBamcheck", "QualityMetric", "Item" ], "display_title":"QualityMetricBamcheck from 2019-08-15" } ], "type":"input" }, "meta":{ "global":true, "type":"QC", "in_path":false } } ], "meta":{ "run_status":"complete", "date_created":"2019-08-15T03:00:58.941422+00:00", "@id":"/workflow-runs-awsem/818236d0-71fe-4116-92b7-d1fb57ae6ef9/", "analysis_step_types":[ "processing" ], "status":"in review by lab", "@type":[ "WorkflowRunAwsem", "WorkflowRun", "Item" ], "display_title":"workflow_gatk-ApplyBQSR-check v9 run 2019-08-15 03:00:58.910422", "workflow":{ "accession":"4DNWFX9UPD4A", "@id":"/workflows/6c9c6f49-f954-4e76-8dfb-d385cddcebd6/", "experiment_types":[ ], "steps":[ { "meta":{ "analysis_step_types":[ "Run gatk ApplyBQSR" ], "software_used":[ "4ae88fb4-23f2-4939-8852-4644069d14d9" ] }, "name":"ApplyBQSR", "outputs":[ { "target":[ { "name":"recalibrated_bam", "step":"integrity-check" } ], "meta":{ "global":true, "file_format":"bam", "cardinality":"single", "type":"data file" }, "name":"recalibrated_bam" } ], "inputs":[ { "meta":{ "global":true, "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "cardinality":"single", "type":"data file" }, "source":[ { "name":"input_bam" } ], "name":"input_bam" }, { "meta":{ "global":true, "file_format":"0cd4e777-a596-4927-95c8-b07716121aa3", "cardinality":"single", "type":"data file" }, "source":[ { "name":"recalibration_report" } ], "name":"recalibration_report" }, { "meta":{ "global":true, "file_format":"5ced774b-a73e-4d1b-8186-d7fbbde7a3c2", "cardinality":"single", "type":"reference file" }, "source":[ { "name":"reference" } ], "name":"reference" }, { "meta":{ "global":true, "cardinality":"single", "type":"parameter" }, "source":[ { "name":"static-quantized-quals_1" } ], "name":"static-quantized-quals_1" }, { "meta":{ "global":true, "cardinality":"single", "type":"parameter" }, "source":[ { "name":"static-quantized-quals_2" } ], "name":"static-quantized-quals_2" }, { "meta":{ "global":true, "cardinality":"single", "type":"parameter" }, "source":[ { "name":"static-quantized-quals_3" } ], "name":"static-quantized-quals_3" } ] }, { "meta":{ "analysis_step_types":[ "Check integrity of output file" ], "software_used":[ "3f2d3b0e-0365-4212-9468-c16ad9531c4d" ] }, "name":"integrity-check", "outputs":[ { "target":[ { "name":"recalibrated_bam-check" } ], "meta":{ "global":true, "cardinality":"single", "type":"QC" }, "name":"recalibrated_bam-check" } ], "inputs":[ { "meta":{ "global":false, "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c", "cardinality":"single", "type":"data file" }, "source":[ { "name":"recalibrated_bam", "step":"ApplyBQSR" } ], "name":"recalibrated_bam" }, { "meta":{ "global":true, "cardinality":"single", "type":"parameter" }, "source":[ { "name":"count" } ], "name":"count" } ] } ], "uuid":"6c9c6f49-f954-4e76-8dfb-d385cddcebd6", "category":[ "processing" ], "@type":[ "Workflow", "Item" ], "display_title":"Run gatk ApplyBQSR plus output integrity-check - 4DNWFX9UPD4A" } } } ]