flowr: Streamlining Design and Deployment of Complex Workflows

Share:

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.

Author
Sahil Seth [aut, cre]
Date of publication
2016-04-19 01:17:29
Maintainer
Sahil Seth <me@sahilseth.com>
License
MIT + file LICENSE
Version
0.9.10
URLs

View on CRAN

Man pages

check
Check consistency of flowdef and flowmat
check_args
Assert none of the arguemnts of a function are null.
create_jobs_mat
create_jobs_mat
error
Error Handler
fetch
Two generic functions to search for pipelines and...
flow
Describing the flow class
flowopts
Default options/params used in flowr and ngsflows
generate_flow_code
generate_flow_code
get_unique_id
get_unique_id
get_wds
Get all the (sub)directories in a folder
job
Describing details of the job object
kill
Kill all jobs submitted to the computing platform, for one or...
plot_flow
Plot a clean and scalable flowchart describing the (work)flow
queue
A 'queue' object defines details regarding how a job is...
replace_slots
replace slots in a S4 object
rerun
Re-run a pipeline in case of hardware or software failures.
run
Run automated Pipelines
setup
Setup and initialize flowr
status
Monitor status of flow(s)
submit_flow
Submit a flow to the cluster
submit_job
Submit a step of a flow
submit_run
Submit several flow objects, limit the max running...
test_queue
test_queue
to_flow
Create flow objects
to_flowdef
Flow Definition defines how to stich steps into a (work)flow.
to_flowdet
Create a flow's submission detail file
to_flowmat
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 desribing this flow

Files in this package

flowr
flowr/inst
flowr/inst/CITATION
flowr/inst/scripts
flowr/inst/scripts/flowr
flowr/inst/scripts/flowr.v1
flowr/inst/scripts/check_file_status.sh
flowr/inst/scripts/show_linkage.R
flowr/inst/conf
flowr/inst/conf/flowr.conf
flowr/inst/conf/torque_comm.sh
flowr/inst/conf/sge.sh
flowr/inst/conf/local.sh
flowr/inst/conf/slurm.sh
flowr/inst/conf/torque.sh
flowr/inst/conf/moab.sh
flowr/inst/conf/lsf.sh
flowr/inst/doc
flowr/inst/doc/flowr_install.R
flowr/inst/doc/flowr_install.html
flowr/inst/doc/flowr_overview.Rmd
flowr/inst/doc/flowr_overview.html
flowr/inst/doc/flowr_tutorial.Rmd
flowr/inst/doc/flowr_tutorial.R
flowr/inst/doc/flowr_tutorial.html
flowr/inst/doc/flowr_overview.R
flowr/inst/doc/flowr_install.Rmd
flowr/inst/pipelines
flowr/inst/pipelines/sleep_pipe.tsv
flowr/inst/pipelines/fastq_bam_bwa.R
flowr/inst/pipelines/sleep_pipe.def
flowr/inst/pipelines/abcd.tsv
flowr/inst/pipelines/sleep_pipe.pdf
flowr/inst/pipelines/sleep_pipe.R
flowr/inst/pipelines/README.md
flowr/inst/pipelines/fastq_bam_bwa.def
flowr/inst/pipelines/fastq_bam_bwa.conf
flowr/inst/pipelines/abcd.def
flowr/tests
flowr/tests/README.md
flowr/tests/testthat.R
flowr/tests/testthat
flowr/tests/testthat/test-checkargs.R
flowr/tests/testthat/test-plots.R
flowr/tests/testthat/test-toflow.R
flowr/NAMESPACE
flowr/NEWS.md
flowr/R
flowr/R/rerun.R
flowr/R/zz-flow-code.R
flowr/R/submit-local.R
flowr/R/to-flowdef.R
flowr/R/check.R
flowr/R/generic.R
flowr/R/fetch.r
flowr/R/conf.R
flowr/R/to-flow.R
flowr/R/plot.R
flowr/R/render-dependency.R
flowr/R/parse-jobids.R
flowr/R/zz-create-jobs-mat.R
flowr/R/errors.R
flowr/R/zz-examples.R
flowr/R/zz-db.R
flowr/R/class-def.R
flowr/R/zz-parse-resources.R
flowr/R/to-flowmat.R
flowr/R/status.R
flowr/R/setup.R
flowr/R/run.R
flowr/R/verbose.R
flowr/R/check-args.R
flowr/R/limit_runs.R
flowr/R/submit-flow.R
flowr/R/rw-flow-details.R
flowr/R/submit-job.R
flowr/R/kill-flow.R
flowr/R/to-flowdet.R
flowr/R/zzz.R
flowr/R/zz-test-queue.R
flowr/vignettes
flowr/vignettes/flowr_tutorial_files
flowr/vignettes/flowr_tutorial_files/figure-html
flowr/vignettes/flowr_tutorial_files/figure-html/plot_skeleton_def-1.png
flowr/vignettes/flowr_tutorial_files/figure-html/plot_tweaked_def-1.png
flowr/vignettes/flowr_overview.Rmd
flowr/vignettes/flowr_tutorial.Rmd
flowr/vignettes/files
flowr/vignettes/files/platforms_supported.txt
flowr/vignettes/files/logo.png
flowr/vignettes/files/flow_def_columns.txt
flowr/vignettes/files/logo_red.png
flowr/vignettes/files/logo_green.png
flowr/vignettes/files/logo_blue.png
flowr/vignettes/files/googl.js
flowr/vignettes/files/toy.png
flowr/vignettes/files/logo_black.png
flowr/vignettes/flowr_overview_files
flowr/vignettes/flowr_overview_files/figure-html
flowr/vignettes/flowr_overview_files/figure-html/plot_one_one-1.png
flowr/vignettes/flowr_overview_files/figure-html/plot_abcd-1.png
flowr/vignettes/flowr_overview_files/figure-html/plotit-1.png
flowr/vignettes/flowr_install.Rmd
flowr/README.md
flowr/MD5
flowr/build
flowr/build/vignette.rds
flowr/DESCRIPTION
flowr/man
flowr/man/verbose.Rd
flowr/man/to_flowdet.Rd
flowr/man/rerun.Rd
flowr/man/run.Rd
flowr/man/flowopts.Rd
flowr/man/status.Rd
flowr/man/write_flow_details.Rd
flowr/man/flow.Rd
flowr/man/get_wds.Rd
flowr/man/queue.Rd
flowr/man/submit_run.Rd
flowr/man/replace_slots.Rd
flowr/man/plot_flow.Rd
flowr/man/test_queue.Rd
flowr/man/whisker_render.Rd
flowr/man/submit_job.Rd
flowr/man/to_flowmat.Rd
flowr/man/generate_flow_code.Rd
flowr/man/to_flowdef.Rd
flowr/man/kill.Rd
flowr/man/check.Rd
flowr/man/create_jobs_mat.Rd
flowr/man/job.Rd
flowr/man/error.Rd
flowr/man/check_args.Rd
flowr/man/get_unique_id.Rd
flowr/man/to_flow.Rd
flowr/man/fetch.Rd
flowr/man/submit_flow.Rd
flowr/man/setup.Rd
flowr/LICENSE