| 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 |
| c | Concatenates Job objects built from the same Task |
| 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... |
| convert_single_quotes_in_cmd | Cleanup cmd |
| cores | Gets cores associated with the jobs in the Job object |
| cores-set | Sets cores associated with the jobs in the Job object |
| dedup | dedup |
| dirs | returns list of character vectors containing the contents of... |
| dot-update_cmd | Create Flow command |
| entities | returns original keyed data.table of entities associated with... |
| ENV_STRING | Default shell command |
| err | returns vector of paths to stderr files associated with this... |
| file.dir | file.dir |
| file.name | file.name |
| Flow | Flow |
| FlowAnnotation | Creates an entity-specific annotation object (ie a path or... |
| FlowAnnotation-class | Class to represent an entity-specific annotation (ie a path... |
| Flow-class | Class representing a collection of tasks |
| 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... |
| Flow-package | Flow: Workflow and task management for genomics pipelines. |
| getcache | getcache |
| getslot | get S4 Slot |
| getslotchain | Get chain of S4 methods |
| gres | Gets queue or partition associated with the jobs in the Job... |
| gres-set | Sets qos associated with the jobs in the Job object |
| ids | returns vector of entity ids associated with this Job objedct |
| inputs | returns keyed data.table of inputs annotation associated with... |
| io_c | Gets ionice -c |
| io_c-set | Sets ionice parameters associated with Job object |
| io_n | Gets ionice -n |
| io_n-set | Sets ionice parameters associated with Job object |
| 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 |
| length | returns length of 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 |
| nice_val | Gets nice value |
| nice_val-set | Sets nice value associated with job object |
| normalizePath | normalizePath |
| 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 |
| plot.Flow | plot.Flow |
| 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 |
| qos-set | Sets qos associated with the jobs in the Job object |
| qprior | Gets qprior value |
| qprior-set | Sets qprior parameter associated with 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... |
| reset.job | reset.job Reset a job with different params |
| rrbind | rrbind |
| run | Runs jobs as local commands from shell via R system calls |
| scmd | Returns vector of ssub (ie Slurm) commands associated with... |
| setwd | changes directory to the directory of the job |
| silent | run expression without any printed output execute expression... |
| sjobs | Tracks down any slurm jobs associated with this Job object... |
| skill | Kills any running Slurm jobs associated with this Job object |
| Slurmize | updates cmd.sh to run on slurm |
| sniff | sniff |
| srun | Runs jobs on Slurm |
| ssub_cmd | ssub_cmd |
| 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... |
| sub-.Flow | Flow subset |
| tailf | tailf |
| task | Object representing a task, which is a wiring of a module... |
| Task-class | S4 class for 'Task' |
| tasks | returns original keyed data.table of entities associated with... |
| time | Gets max time limit associated with job object |
| time-set | Sets max time limit associated with the jobs in the Job... |
| update | updates Job status This method checks inputs for updates to... |
| viewtask | or Flow Task object |
| xml2task | Makes a best attempt to convert a firehose xml task... |
