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.

Install the latest version of this package by entering the following in R:
install.packages("flowr")
AuthorSahil Seth [aut, cre]
Date of publication2016-04-19 01:17:29
MaintainerSahil Seth <me@sahilseth.com>
LicenseMIT + file LICENSE
Version0.9.10
https://github.com/sahilseth/flowr

View on CRAN

Functions

as.flowdef Man page
as.flowmat Man page
check Man page
check_args Man page
check.flowdef Man page
check.flowmat Man page
create_jobs_mat Man page
definition Man page
error Man page
fetch Man page
fetch_conf Man page
fetch_pipes Man page
flow Man page
flow-class Man page
flowdef Man page
flowopts Man page
flowr Man page
generate_flow_code Man page
get_opts Man page
get_status Man page
get_status.character Man page
get_status.data.frame Man page
get_status.flow Man page
get_unique_id Man page
get_wds Man page
is.flow Man page
is.flowdef Man page
is.flowmat Man page
job Man page
kill Man page
kill.character Man page
kill.flow Man page
load_opts Man page
opts_flow Man page
opts_flow$get Man page
opts_flow$load Man page
opts_flow$set Man page
plot_flow Man page
plot.flow Man page
plot_flow.character Man page
plot.flowdef Man page
plot_flow.flow Man page
plot_flow.flowdef Man page
plot_flow.list Man page
queue Man page
queue-class Man page
replace_slots Man page
rerun Man page
rerun.character Man page
rerun.flow Man page
run Man page
run_flow Man page
run_pipe Man page
set_opts Man page
setup Man page
status Man page
submit_flow Man page
submit_flow.flow Man page
submit_flow.list Man page
submit_job Man page
submit_run Man page
test_queue Man page
to_flow Man page
to_flow.character Man page
to_flow.data.frame Man page
to_flowdef Man page
to_flowdef.character Man page
to_flowdef.flow Man page
to_flowdef.flowmat Man page
to_flowdet Man page
to_flowdet.character Man page
to_flowdet.flow Man page
to_flowdet.rootdir Man page
to_flow.flowmat Man page
to_flow.list Man page
to_flowmat Man page
to_flowmat.data.frame Man page
to_flowmat.flow Man page
to_flowmat.list Man page
verbose Man page
whisker_render Man page
write_flow_details Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.