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.

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

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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

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

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