Build Status cran downloads Streamlining Computing workflows

Latest documentation:

Flowr 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.




A few lines, to get started

## Official stable release from CRAN (updated every other month)
## visit for more details
install.packages("flowr",  repos = "")

# or a latest version from DRAT, provide cran for dependencies
install.packages("flowr", repos = c(CRAN="", DRAT=""))

library(flowr) ## load the library
setup() ## copy flowr bash script; and create a folder flowr under home.

# Run an example pipeline

# style 1: sleep_pipe() function creates system cmds
flowr run x=sleep_pipe platform=local execute=TRUE

# style 2: we start with a tsv of system cmds
# get example files
wget --no-check-certificate
wget --no-check-certificate

# submit to local machine
flowr to_flow x=sleep_pipe.tsv def=sleep_pipe.def platform=local execute=TRUE
# submit to local LSF cluster
flowr to_flow x=sleep_pipe.tsv def=sleep_pipe.def platform=lsf execute=TRUE

Example pipelines inst/pipelines



This package is under active-development, you may watch for changes using the watch link above.


Please feel free to raise a github issue with questions and comments.