Man pages for mskilab/Flow
Workflow and task management for genomics pipelines.
| as.character | Convert task object to character, can be dumped to file and... |
| bcmd | Returns vector of bsub (ie LSF) commands associated with this... |
| bjobs | Tracks down any LSF jobs associated with this Job object... |
| bkill | Kills any running LSF jobs associated with this Job object |
| brun | Runs jobs on LSF |
| bsub_cmd | bsub_cmd |
| cache | caches .rds copy of job object to standard location... |
| chmod | chmods Job output directories Chmods outputs of jobs (by... |
| cmd | Gets vector of command line calls associated with the jobs in... |
| dedup | dedup |
| dirs | returns list of character vectors containing the contents of... |
| entities | returns original keyed data.table of entities associated with... |
| err | returns vector of paths to stderr files associated with this... |
| file.dir | file.dir |
| file.name | file.name |
| FlowAnnotation | Creates an entity-specific annotation object (ie a path or... |
| FlowLiteral | Creates object representing a literal argument to a task (ie... |
| FlowLiteral-class | Class to represent a literal argument to a task (ie a static... |
| FlowOutput | Constructs an object representing the wiring of a regexp on a... |
| FlowOutput-class | Class representing the wiring of a regexp on a job output... |
| ids | returns vector of entity ids associated with this Job objedct |
| inputs | returns keyed data.table of inputs annotation associated with... |
| jname | Returns character vector of job names associated with this... |
| Job | Constructs a job object from a Task and keyed data.table of... |
| Job-class | Class representing a set of jobs, each which is the... |
| key | Retrieves the entity key associated with this Job object |
| mem | Gets max memory associated with the jobs in the Job object |
| mem-set | Sets max memory associated with the jobs in the Job object |
| Module | Class to implement modules, which are standalone pieces of... |
| Module-class | Module class |
| module-task | Gets module associated with a Task |
| more | more |
| now | Toggles whether to force jobs to run now |
| now-set | Sets now param associated with the jobs in the Job object |
| out | returns vector of paths to stdout files associated with this... |
| outdir | Gets vector of output directories associated with the jobs in... |
| outputs | returns keyed data.table of output entity annotations... |
| parse.info | parse.info |
| purge | purges all output / run directories associated with this Job... |
| qcmd | Returns vector of qsub (ie SGE) commands associated with this... |
| qjobs | Tracks down any sGE jobs associated with this Job object... |
| qkill | Kills any running SGE jobs associated with this Job object |
| qrun | Runs jobs on LSF |
| qsub_cmd | qsub_cmd |
| queue | Gets queue associated with the jobs in the Job object |
| queue-set | Sets queue associated with the jobs in the Job object |
| refresh | refreshes .rds copy of job object from standard location... |
| report | Retrieves a data.table reporting detailed runtime stats... |
| run | Runs jobs as local commands from shell via R system calls |
| status | Returns character vector of status of jobs in this Job... |
| status.info | returns vector of more detailed statuses associated with jobs... |
| sub | caches .rds copy of job object to standard location... |
| tailf | tailf |
| Task | Object representing a task, which is a wiring of a module... |
| Task-class | S4 class for 'Task' |
| update | updates Job status This method checks inputs for updates to... |
| xml2task | Makes a best attempt to convert a firehose xml task... |
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