Package: flowr 0.9.11

Sahil Seth

flowr: Streamlining Design and Deployment of Complex Workflows

This framework allows you to design and implement complex pipelines, and deploy them on your institution's computing cluster. This has been built keeping in mind the needs of bioinformatics workflows. However, it is easily extendable to any field where a series of steps (shell commands) are to be executed in a (work)flow.

Authors:Sahil Seth [aut, cre]

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flowr.pdf |flowr.html✨
flowr/json (API)
NEWS

# Install 'flowr' in R:
install.packages('flowr', repos = c('https://flow-r.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/flow-r/flowr/issues

On CRAN:

bioinformaticscloudclusterflowrpipelinetsvworkflow

40 exports 83 stars 3.90 score 32 dependencies 1 mentions 60 scripts 298 downloads

Last updated 4 years agofrom:dabf9d0df4. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 13 2024
R-4.5-winNOTESep 13 2024
R-4.5-linuxNOTESep 13 2024
R-4.4-winNOTESep 13 2024
R-4.4-macNOTESep 13 2024
R-4.3-winOKSep 13 2024
R-4.3-macOKSep 13 2024

Exports:as.flowdefas.flowmatcheckcheck_argsfetchfetch_conffetch_pipesflowflowoptsget_optsget_resourcesget_resources_lsfget_statusget_unique_idget_wdsis.flowis.flowdefis.flowmatjobkillload_optsopts_flowplot_flowqueuererunrunrun_piperun_pipe_v2set_optssetupstatussubmit_flowsubmit_runtest_queueto_df.statusto_flowto_flowdefto_flowdetto_flowmatwhisker_render

Dependencies:bitbit64clicliprcpp11crayondiagramfansigluehmslifecyclemagrittrparamspillarpkgconfigprettyunitsprogresspurrrR6RcppRcppTOMLreadrrlangshapetibbletidyselecttzdbutf8vctrsvroomwhiskerwithr

flowr

Sahil Seth

Rendered fromflowr_install.Rmdusingknitr::rmarkdownon Sep 13 2024.

Last update: 2021-03-02
Started: 2015-09-25

flowr

Sahil Seth

Rendered fromflowr_overview.Rmdusingknitr::rmarkdownon Sep 13 2024.

Last update: 2021-03-02
Started: 2015-09-25

flowr

Sahil Seth

Rendered fromflowr_tutorial.Rmdusingknitr::rmarkdownon Sep 13 2024.

Last update: 2021-03-02
Started: 2015-09-25

Readme and manuals

Help Manual

Help pageTopics
Check consistency of flowdef and flowmatcheck check.flowdef check.flowmat
Assert none of the arguments of a function are null.check_args
Two generic functions to search for pipelines and configuration files.fetch fetch_conf fetch_pipes
Describing the flow classflow flow-class
Default options/params used in flowr and ngsflowsflowopts get_opts load_opts opts_flow opts_flow$get opts_flow$load opts_flow$set set_opts
Extract resources used by each job of a flow get_resources currently this only works on LSFget_resources
Get all the (sub)directories in a folderget_wds
Describing details of the job objectjob
Kill all jobs submitted to the computing platform, for one or multiple flowskill kill.character kill.flow
Plot a clean and scalable flowchart describing the (work)flowplot plot.flow plot.flowdef plot_flow plot_flow.character plot_flow.flow plot_flow.flowdef plot_flow.list
A 'queue' object defines details regarding how a job is submittedqueue queue-class
Re-run a pipeline in case of hardware or software failures.rerun rerun.character rerun.flow
Run automated Pipelinesrun run_flow run_pipe
Run automated Pipelinesrun_pipe_v2
Setup and initialize flowrsetup
Monitor status of flow(s)get_status get_status.character get_status.data.frame get_status.flow status
Submit a flow to the clustersubmit_flow submit_flow.flow submit_flow.list
Submit a step of a flowsubmit_job
Submit several flow objects, limit the max running concurrentlysubmit_run
test_queuetest_queue
to_df.statusto_df.status
Create flow objectsflowr is.flow to_flow to_flow.character to_flow.data.frame to_flow.flowmat to_flow.list
Flow Definition defines how to stitch steps into a (work)flow.as.flowdef definition flowdef is.flowdef to_flowdef to_flowdef.character to_flowdef.flow to_flowdef.flowmat
Create a flow's submission detail fileto_flowdet to_flowdet.character to_flowdet.flow to_flowdet.rootdir
Create a flowmat using a list a commands.as.flowmat is.flowmat to_flowmat to_flowmat.data.frame to_flowmat.flow to_flowmat.list
Verbose levels, defining verboseness of messagesverbose
Wrapper around whisker.render with some additional checkswhisker_render
Write files describing this flowwrite_flow_details