Streamlining Design and Deployment of Complex Workflows

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Documentation for package ‘flowr’ version 0.9.11

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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