# Streamlining Design and Deployment of Complex Workflows

## Documentation for package ‘flowr’ version 0.9.11

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

as.flowdef | Flow Definition defines how to stitch steps into a (work)flow.
as.flowmat | Create a flowmat using a list a commands.
check | Check consistency of flowdef and flowmat
check.flowdef | Check consistency of flowdef and flowmat
check.flowmat | Check consistency of flowdef and flowmat
check_args | Assert none of the arguments of a function are null.
definition | Flow Definition defines how to stitch steps into a (work)flow.
fetch | Two generic functions to search for pipelines and configuration files.
fetch_conf | Two generic functions to search for pipelines and configuration files.
fetch_pipes | Two generic functions to search for pipelines and configuration files.
flow | Describing the flow class
flow-class | Describing the flow class
flowdef | Flow Definition defines how to stitch steps into a (work)flow.
flowopts | Default options/params used in flowr and ngsflows
flowr | Create flow objects
get_opts | Default options/params used in flowr and ngsflows
get_resources | Extract resources used by each job of a flow get_resources currently this only works on LSF
get_status | Monitor status of flow(s)
get_status.character | Monitor status of flow(s)
get_status.data.frame | Monitor status of flow(s)
get_status.flow | Monitor status of flow(s)
get_wds | Get all the (sub)directories in a folder
is.flow | Create flow objects
is.flowdef | Flow Definition defines how to stitch steps into a (work)flow.
is.flowmat | Create a flowmat using a list a commands.
job | Describing details of the job object
kill | Kill all jobs submitted to the computing platform, for one or multiple flows
kill.character | Kill all jobs submitted to the computing platform, for one or multiple flows
kill.flow | Kill all jobs submitted to the computing platform, for one or multiple flows
load_opts | Default options/params used in flowr and ngsflows
opts_flow | Default options/params used in flowr and ngsflows
opts_flow$get | Default options/params used in flowr and ngsflows
opts_flow$load | Default options/params used in flowr and ngsflows
opts_flow$set | Default options/params used in flowr and ngsflows
plot | Plot a clean and scalable flowchart describing the (work)flow
plot.flow | Plot a clean and scalable flowchart describing the (work)flow
plot.flowdef | Plot a clean and scalable flowchart describing the (work)flow
plot_flow | Plot a clean and scalable flowchart describing the (work)flow
plot_flow.character | Plot a clean and scalable flowchart describing the (work)flow
plot_flow.flow | Plot a clean and scalable flowchart describing the (work)flow
plot_flow.flowdef | Plot a clean and scalable flowchart describing the (work)flow
plot_flow.list | Plot a clean and scalable flowchart describing the (work)flow
queue | A 'queue' object defines details regarding how a job is submitted
queue-class | A 'queue' object defines details regarding how a job is submitted
rerun | Re-run a pipeline in case of hardware or software failures.
rerun.character | Re-run a pipeline in case of hardware or software failures.
rerun.flow | Re-run a pipeline in case of hardware or software failures.
run | Run automated Pipelines
run_flow | Run automated Pipelines
run_pipe | Run automated Pipelines
run_pipe_v2 | Run automated Pipelines
setup | Setup and initialize flowr
set_opts | Default options/params used in flowr and ngsflows
status | Monitor status of flow(s)
submit_flow | Submit a flow to the cluster
submit_flow.flow | Submit a flow to the cluster
submit_flow.list | Submit a flow to the cluster
submit_job | Submit a step of a flow
submit_run | Submit several flow objects, limit the max running concurrently
test_queue | test_queue
to_df.status | to_df.status
to_flow | Create flow objects
to_flow.character | Create flow objects
to_flow.data.frame | Create flow objects
to_flow.flowmat | Create flow objects
to_flow.list | Create flow objects
to_flowdef | Flow Definition defines how to stitch steps into a (work)flow.
to_flowdef.character | Flow Definition defines how to stitch steps into a (work)flow.
to_flowdef.flow | Flow Definition defines how to stitch steps into a (work)flow.
to_flowdef.flowmat | Flow Definition defines how to stitch steps into a (work)flow.
to_flowdet | Create a flow's submission detail file
to_flowdet.character | Create a flow's submission detail file
to_flowdet.flow | Create a flow's submission detail file
to_flowdet.rootdir | Create a flow's submission detail file
to_flowmat | Create a flowmat using a list a commands.
to_flowmat.data.frame | Create a flowmat using a list a commands.
to_flowmat.flow | Create a flowmat using a list a commands.
to_flowmat.list | Create a flowmat using a list a commands.
verbose | Verbose levels, defining verboseness of messages
whisker_render | Wrapper around whisker.render with some additional checks
write_flow_details | Write files describing this flow