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one or more run parameters.\nMany parameters will be set to a default value.\nTo see all parameter options available, click the gear cog next to the substep titled with the workflow name.\nFor a full list of the parameters and their descriptions, see ",{"type":430,"tag":650,"props":747,"children":748},{},[749],{"type":435,"value":750},"Inputs",{"type":435,"value":752}," table on the documentation page for the workflow that you are running.\nBelow is an example showing how to customize parameters for the Neoepitope Prediction workflow.",{"type":430,"tag":431,"props":754,"children":755},{},[756],{"type":430,"tag":630,"props":757,"children":760},{"alt":758,"src":759},"change parameters","/img/genomics-platform/analyzing-data/running-our-workflows/change-parameters.gif",[],{"type":430,"tag":735,"props":762,"children":764},{"id":763},"hooking-up-inputs",[765],{"type":435,"value":766},"Hooking up Inputs",{"type":430,"tag":431,"props":768,"children":769},{},[770,772,778,780,787,789,795],{"type":435,"value":771},"Next, you'll need to hook up the input files you uploaded in  ",{"type":430,"tag":438,"props":773,"children":775},{"href":774},"#uploading-files",[776],{"type":435,"value":777},"the upload files section",{"type":435,"value":779},".\nIn the example below, we are running the Rapid RNA-Seq workflow using the FASTQ version of the pipeline.\nThe example gif shows  that you hook up the inputs by clicking on the ",{"type":430,"tag":781,"props":782,"children":784},"code",{"className":783},[],[785],{"type":435,"value":786},"Fastq/R1",{"type":435,"value":788}," and ",{"type":430,"tag":781,"props":790,"children":792},{"className":791},[],[793],{"type":435,"value":794},"Fastq/R2",{"type":435,"value":796}," slots and selecting the respective input files.\nThis process is similar for all workflows.",{"type":430,"tag":431,"props":798,"children":799},{},[800],{"type":430,"tag":630,"props":801,"children":804},{"alt":802,"src":803},"hookup inputs","/img/genomics-platform/analyzing-data/running-our-workflows/hookup-inputs.gif",[],{"type":430,"tag":735,"props":806,"children":808},{"id":807},"starting-the-workflow",[809],{"type":435,"value":810},"Starting the Workflow",{"type":430,"tag":431,"props":812,"children":813},{},[814,816,821],{"type":435,"value":815},"Once your input files are hooked up, you should be able to start the workflow by clicking the ",{"type":430,"tag":650,"props":817,"children":818},{},[819],{"type":435,"value":820},"Run as Analysis...",{"type":435,"value":822}," button in the top right hand corner of the workflow dialog.\nSee the example below using the Rapid RNA-Seq workflow.",{"type":430,"tag":431,"props":824,"children":825},{},[826],{"type":430,"tag":630,"props":827,"children":830},{"alt":828,"src":829},"run analysis","/img/genomics-platform/analyzing-data/running-our-workflows/run-analysis.gif",[],{"type":430,"tag":641,"props":832,"children":834},{"color":643,"icon":833},"i-heroicons-light-bulb",[835],{"type":430,"tag":431,"props":836,"children":837},{},[838,843,846,848,851,853,857],{"type":430,"tag":650,"props":839,"children":840},{},[841],{"type":435,"value":842},"Tip",{"type":430,"tag":656,"props":844,"children":845},{},[],{"type":435,"value":847},"\nIf you cannot click this button, please ensure that all of the inputs are correctly hooked up.",{"type":430,"tag":656,"props":849,"children":850},{},[],{"type":435,"value":852},"\nIf you're still have trouble, please reach out to ",{"type":430,"tag":438,"props":854,"children":855},{"href":675},[856],{"type":435,"value":678},{"type":435,"value":858}," and include a screenshot of the workflow screen above.",{"type":430,"tag":465,"props":860,"children":862},{"id":861},"monitoring-run-progress",[863],{"type":435,"value":864},"Monitoring Run Progress",{"type":430,"tag":431,"props":866,"children":867},{},[868],{"type":435,"value":869},"Once you have started one or more workflow runs, you can safely close your browser and come back later to check the status of the jobs.\nTo do this, navigate to the landing page of the workflow that you want to check.\nNext, click \"View Results\" then select the \"View Running Jobs\" option.\nYou will be redirected to the job monitoring page in your DNAnexus workspace.\nEach job you kicked off gets one row in this table.\nSee the two examples below for the Rapid RNA-Seq workflow.",{"type":430,"tag":431,"props":871,"children":872},{},[873],{"type":430,"tag":630,"props":874,"children":877},{"alt":875,"src":876},"view results","/img/genomics-platform/analyzing-data/running-our-workflows/workflow_view-results_example.gif",[],{"type":430,"tag":431,"props":879,"children":880},{},[881],{"type":435,"value":882},"You can click the \"+\" on any of the runs to check the status of individual steps of the workflow.\nOther information, such as time, cost of individual steps in the workflow, and even viewing the job logs can accessed by clicking around the sub-items.",{"type":430,"tag":431,"props":884,"children":885},{},[886],{"type":430,"tag":630,"props":887,"children":890},{"alt":888,"src":889},"job detailed view","/img/genomics-platform/analyzing-data/running-our-workflows/job-detailed-view.gif",[],{"type":430,"tag":641,"props":892,"children":893},{"color":643,"icon":833},[894],{"type":430,"tag":431,"props":895,"children":896},{},[897,901,904,906,913],{"type":430,"tag":650,"props":898,"children":899},{},[900],{"type":435,"value":842},{"type":430,"tag":656,"props":902,"children":903},{},[],{"type":435,"value":905},"\nRefer to the ",{"type":430,"tag":438,"props":907,"children":910},{"href":908,"rel":909},"https://documentation.dnanexus.com/user/running-apps-and-workflows/monitoring-executions",[442],[911],{"type":435,"value":912},"DNAnexus Monitoring Executions Documentation",{"type":435,"value":914}," for advanced capabilities for monitoring jobs.",{"type":430,"tag":465,"props":916,"children":918},{"id":917},"accessing-results",[919],{"type":435,"value":920},"Accessing Results",{"type":430,"tag":735,"props":922,"children":924},{"id":923},"custom-visualizations",[925],{"type":435,"value":926},"Custom Visualizations",{"type":430,"tag":431,"props":928,"children":929},{},[930],{"type":435,"value":931},"Most workflows in St. Jude Cloud produce one or more visualizations that helps you to understand the raw results.",{"type":430,"tag":431,"props":933,"children":934},{},[935],{"type":435,"value":936},"To access the visualization(s), navigate to the landing page of the workflow that you want to check.\nNext, click \"View Results\" then select the \"Visualize Results\" option.",{"type":430,"tag":431,"props":938,"children":939},{},[940],{"type":430,"tag":630,"props":941,"children":944},{"alt":942,"src":943},"Click \"Visualize Results\"","/img/genomics-platform/analyzing-data/running-our-workflows/workflow_VisualizeReults_example.gif",[],{"type":430,"tag":431,"props":946,"children":947},{},[948],{"type":435,"value":949},"You should now see a list of visualization files.\nClick on a visualization name to explore.",{"type":430,"tag":431,"props":951,"children":952},{},[953],{"type":435,"value":954},"Below is a brief description of two of our custom visualizations.",{"type":430,"tag":956,"props":957,"children":959},"h4",{"id":958},"proteinpaint-bigwig-viewer",[960],{"type":435,"value":961},"ProteinPaint BigWig Viewer",{"type":430,"tag":431,"props":963,"children":964},{},[965],{"type":435,"value":966},"The ProteinPaint interactive coverage viewer is used to visualize any bigWig file.\nYou can follow these steps to get an understanding of how it works.",{"type":430,"tag":968,"props":969,"children":970},"ol",{},[971,976,989],{"type":430,"tag":481,"props":972,"children":973},{},[974],{"type":435,"value":975},"Open up the custom viewer file output by your pipeline.\nThe name of this file will vary, so consult the specific pipeline guide to know where to find it.",{"type":430,"tag":481,"props":977,"children":978},{},[979,981,984],{"type":435,"value":980},"Click \"Launch\" in the bottom right corner to launch the custom viewer.",{"type":430,"tag":656,"props":982,"children":983},{},[],{"type":430,"tag":630,"props":985,"children":988},{"alt":986,"src":987},"bigwig viewer startup","/img/genomics-platform/analyzing-data/running-our-workflows/bigwig_viewer_startup.png",[],{"type":430,"tag":481,"props":990,"children":991},{},[992,994,997],{"type":435,"value":993},"Once the page has loaded, you will be able to see the bigWig viewer.\nYou can navigate around the genome by gene or genomic location.\nAlongside the coverage track is the GENCODE gene reference.",{"type":430,"tag":656,"props":995,"children":996},{},[],{"type":430,"tag":630,"props":998,"children":1001},{"alt":999,"src":1000},"bigwig detail","/img/genomics-platform/analyzing-data/running-our-workflows/bigwig_detail.png",[],{"type":430,"tag":956,"props":1003,"children":1005},{"id":1004},"proteinpaint-fusion-viewer",[1006],{"type":435,"value":1007},"ProteinPaint Fusion Viewer",{"type":430,"tag":431,"props":1009,"children":1010},{},[1011],{"type":435,"value":1012},"The ProteinPaint interactive fusion viewer is used to visualize putative fusions called by Rapid RNA-Seq.\nYou can follow these steps to get an understanding of how it works.",{"type":430,"tag":968,"props":1014,"children":1015},{},[1016,1020,1033,1046,1059],{"type":430,"tag":481,"props":1017,"children":1018},{},[1019],{"type":435,"value":975},{"type":430,"tag":481,"props":1021,"children":1022},{},[1023,1025,1028],{"type":435,"value":1024},"Click \"Launch\" in the bottom right corner to launch the custom\nviewer.",{"type":430,"tag":656,"props":1026,"children":1027},{},[],{"type":430,"tag":630,"props":1029,"children":1032},{"alt":1030,"src":1031},"fusions viewer startup","/img/genomics-platform/analyzing-data/running-our-workflows/fusions_viewer_startup.png",[],{"type":430,"tag":481,"props":1034,"children":1035},{},[1036,1038,1041],{"type":435,"value":1037},"Once the page has finished loading, you will be presented with a summary of all of the fusions produced by the pipeline.\nEach bullet point is a separate category for the structural variants, with the more interesting fusions at the top.\nClick one of the categories to view the fusions in that category.",{"type":430,"tag":656,"props":1039,"children":1040},{},[],{"type":430,"tag":630,"props":1042,"children":1045},{"alt":1043,"src":1044},"fusions click hq","/img/genomics-platform/analyzing-data/running-our-workflows/fusions_click_hq.png",[],{"type":430,"tag":481,"props":1047,"children":1048},{},[1049,1051,1054],{"type":435,"value":1050},"You can see all of the fusions in that category are now listed on the screen.\nHover over one of the fusions to see the detailed view.",{"type":430,"tag":656,"props":1052,"children":1053},{},[],{"type":430,"tag":630,"props":1055,"children":1058},{"alt":1056,"src":1057},"fusions hover","/img/genomics-platform/analyzing-data/running-our-workflows/fusions_hover.png",[],{"type":430,"tag":481,"props":1060,"children":1061},{},[1062,1064,1067],{"type":435,"value":1063},"The popup contains a large amount of information that might be interesting to you based on your use case, such as the transcript and other metrics like read counts, quality metrics, and recurrence.",{"type":430,"tag":656,"props":1065,"children":1066},{},[],{"type":430,"tag":630,"props":1068,"children":1071},{"alt":1069,"src":1070},"fusions detail","/img/genomics-platform/analyzing-data/running-our-workflows/fusions_detail.png",[],{"type":430,"tag":735,"props":1073,"children":1075},{"id":1074},"raw-results-files",[1076],{"type":435,"value":1077},"Raw Results Files",{"type":430,"tag":431,"props":1079,"children":1080},{},[1081],{"type":435,"value":1082},"If additionally, you would like to view raw output files, you may do so by following the directions below.",{"type":430,"tag":431,"props":1084,"children":1085},{},[1086],{"type":435,"value":1087},"To access the raw output file, navigate to the landing page of the workflow that you want to check.\nNext, click \"View Results\" then select the \"View Results Files\" option.",{"type":430,"tag":431,"props":1089,"children":1090},{},[1091],{"type":430,"tag":630,"props":1092,"children":1095},{"alt":1093,"src":1094},"Click \"View Results Files\"","/img/genomics-platform/analyzing-data/running-our-workflows/workflow_Raw-results_example.gif",[],{"type":430,"tag":431,"props":1097,"children":1098},{},[1099],{"type":435,"value":1100},"You should now be in the file system view of your workflow's workspace in DNAnexus with access to files that you uploaded as well as results files that are generated.\nSee the example file system view below for the Rapid RNA-Seq workflow.",{"type":430,"tag":431,"props":1102,"children":1103},{},[1104],{"type":430,"tag":630,"props":1105,"children":1108},{"alt":1106,"src":1107},"rapid rna seq results","/img/genomics-platform/analyzing-data/running-our-workflows/rapid-rna-results.png",[],{"type":430,"tag":431,"props":1110,"children":1111},{},[1112],{"type":435,"value":1113},"This is similar to your the file system on your computer, and you can do many common operations such as deleting, renaming, and moving files.\nHow/where the result files are generated are specific to each pipeline.\nPlease refer to your individual workflow's documentation on where the output files are kept.",{"type":430,"tag":431,"props":1115,"children":1116},{},[1117,1119,1123],{"type":435,"value":1118},"If you have any unanswered questions about how to run one of our in-house workflows, please reach out to ",{"type":430,"tag":438,"props":1120,"children":1121},{"href":675},[1122],{"type":435,"value":678},{"type":435,"value":680},{"type":430,"tag":465,"props":1125,"children":1127},{"id":1126},"similar-topics",[1128],{"type":435,"value":1129},"Similar Topics",{"type":430,"tag":431,"props":1131,"children":1132},{},[1133,1137,1140,1145,1148],{"type":430,"tag":438,"props":1134,"children":1135},{"href":86},[1136],{"type":435,"value":85},{"type":430,"tag":656,"props":1138,"children":1139},{},[],{"type":430,"tag":438,"props":1141,"children":1142},{"href":67},[1143],{"type":435,"value":1144},"Working with our Data Overview",{"type":430,"tag":656,"props":1146,"children":1147},{},[],{"type":430,"tag":438,"props":1149,"children":1150},{"href":70},[1151],{"type":435,"value":69},{"title":424,"searchDepth":1153,"depth":1153,"links":1154},2,[1155,1156,1157,1163,1164,1168],{"id":467,"depth":1153,"text":470},{"id":683,"depth":1153,"text":686},{"id":705,"depth":1153,"text":708,"children":1158},[1159,1161,1162],{"id":737,"depth":1160,"text":740},3,{"id":763,"depth":1160,"text":766},{"id":807,"depth":1160,"text":810},{"id":861,"depth":1153,"text":864},{"id":917,"depth":1153,"text":920,"children":1165},[1166,1167],{"id":923,"depth":1160,"text":926},{"id":1074,"depth":1160,"text":1077},{"id":1126,"depth":1153,"text":1129},"markdown","content:3.genomics-platform:4.analyzing-data:2.running-our-workflows.md","content","3.genomics-platform/4.analyzing-data/2.running-our-workflows.md","3.genomics-platform/4.analyzing-data/2.running-our-workflows","md",[1176,1178],{"_path":86,"title":85,"description":1177},"Before you begin interacting with St. Jude Cloud Platform from the command line, you'll need to understand some details on the underlying architecture of the platform.\nThe St. Jude Cloud Platform is built on top of a genomics cloud ecosystem provided by DNAnexus.",{"_path":92,"title":91,"description":1179},"This guide will take you through the process of writing an application for working with and manipulating the St. Jude data you've requested.\nBy creating your own application, you will be able to wrap genomic tools and packages from external sources, as well as any tool or application you might have written yourself.",1791243633003]