Man pages for mskilab/Flow
Workflow and task management for genomics pipelines.

as.characterConvert task object to character, can be dumped to file and...
bcmdReturns vector of bsub (ie LSF) commands associated with this...
bjobsTracks down any LSF jobs associated with this Job object...
bkillKills any running LSF jobs associated with this Job object
brunRuns jobs on LSF
bsub_cmdbsub_cmd
cachecaches .rds copy of job object to standard location...
chmodchmods Job output directories Chmods outputs of jobs (by...
cmdGets vector of command line calls associated with the jobs in...
dedupdedup
dirsreturns list of character vectors containing the contents of...
entitiesreturns original keyed data.table of entities associated with...
errreturns vector of paths to stderr files associated with this...
file.dirfile.dir
file.namefile.name
FlowAnnotationCreates an entity-specific annotation object (ie a path or...
FlowLiteralCreates object representing a literal argument to a task (ie...
FlowLiteral-classClass to represent a literal argument to a task (ie a static...
FlowOutputConstructs an object representing the wiring of a regexp on a...
FlowOutput-classClass representing the wiring of a regexp on a job output...
idsreturns vector of entity ids associated with this Job objedct
inputsreturns keyed data.table of inputs annotation associated with...
jnameReturns character vector of job names associated with this...
JobConstructs a job object from a Task and keyed data.table of...
Job-classClass representing a set of jobs, each which is the...
keyRetrieves the entity key associated with this Job object
memGets max memory associated with the jobs in the Job object
mem-setSets max memory associated with the jobs in the Job object
ModuleClass to implement modules, which are standalone pieces of...
Module-classModule class
module-taskGets module associated with a Task
moremore
nowToggles whether to force jobs to run now
now-setSets now param associated with the jobs in the Job object
outreturns vector of paths to stdout files associated with this...
outdirGets vector of output directories associated with the jobs in...
outputsreturns keyed data.table of output entity annotations...
parse.infoparse.info
purgepurges all output / run directories associated with this Job...
qcmdReturns vector of qsub (ie SGE) commands associated with this...
qjobsTracks down any sGE jobs associated with this Job object...
qkillKills any running SGE jobs associated with this Job object
qrunRuns jobs on LSF
qsub_cmdqsub_cmd
queueGets queue associated with the jobs in the Job object
queue-setSets queue associated with the jobs in the Job object
refreshrefreshes .rds copy of job object from standard location...
reportRetrieves a data.table reporting detailed runtime stats...
runRuns jobs as local commands from shell via R system calls
statusReturns character vector of status of jobs in this Job...
status.inforeturns vector of more detailed statuses associated with jobs...
subcaches .rds copy of job object to standard location...
tailftailf
TaskObject representing a task, which is a wiring of a module...
Task-classS4 class for 'Task'
updateupdates Job status This method checks inputs for updates to...
xml2taskMakes a best attempt to convert a firehose xml task...
mskilab/Flow documentation built on May 19, 2018, 9:10 a.m.