Streamlining Design and Deployment of Complex Workflows
Check consistency of flowdef and flowmat
Assert none of the arguments of a function are null.
create_jobs_mat
Error Handler
Two generic functions to search for pipelines and configuration files.
Describing the flow class
Default options/params used in flowr and ngsflows
generate_flow_code
Extract resources used by each job of a flow get_resources currently t...
get_resources_lsf
get_unique_id
Get all the (sub)directories in a folder
Describing details of the job object
Kill all jobs submitted to the computing platform, for one or multiple...
Plot a clean and scalable flowchart describing the (work)flow
A queue object defines details regarding how a job is submitted
replace slots in a S4 object
Re-run a pipeline in case of hardware or software failures.
Run automated Pipelines
Run automated Pipelines
Setup and initialize flowr
Monitor status of flow(s)
Submit a flow to the cluster
Submit a step of a flow
Submit several flow objects, limit the max running concurrently
test_queue
to_df.status
Create flow objects
Flow Definition defines how to stitch steps into a (work)flow.
Create a flow's submission detail file
Create a flowmat using a list a commands.
Verbose levels, defining verboseness of messages
Wrapper around whisker.render with some additional checks
Write files describing this flow
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.