flowr (version 0.9.11)

flowopts: Default options/params used in flowr and ngsflows

Description

There are three helper functions which attempt to manage parameters used by flowr and ngsflows:

• get_opts OR opts_flow\$get(): show all default options

• set_opts OR opts_flow\$set(): set default options

• load_opts OR opts_flow\$load(): load options specified in a tab separated text file

For more details regarding these functions refer to params package.

Usage

flowopts
get_opts(...)
set_opts(...)
load_opts(...)

Arguments

...

• get: names of options to fetch

• set: a set of options in a name=value format separated by commas

Format

opts_flow

An object of class list of length 5.

Details

By default flowr loads, ~/flowr/conf/flowr.conf and ~/flowr/conf/ngsflows.conf

Below is a list of default flowr options, retrieved via

opts_flow$get():

|name              |value                    |
|:-----------------|:------------------------|
|default_regex     |(.*)                     |
|flow_base_path    |~/flowr                  |
|flow_conf_path    |~/flowr/conf             |
|flow_parse_lsf    |.*(\<[0-9]*\>).*         |
|flow_parse_moab   |(.*)                     |
|flow_parse_sge    |(.*)                     |
|flow_parse_slurm  |(.*)                     |
|flow_parse_torque |(.?)\..*                 |
|flow_pipe_paths   |~/flowr/pipelines        |
|flow_pipe_urls    |~/flowr/pipelines        |
|flow_platform     |local                    |
|flow_run_path     |~/flowr/runs             |
|my_conf_path      |~/flowr/conf             |
|my_dir            |path/to/a/folder         |
|my_path           |~/flowr                  |
|my_tool_exe       |/usr/bin/ls              |
|time_format       |%a %b %e %H:%M:%S CDT %Y |
|verbose           |FALSE                    |

See Also

fetch params read_sheet

Examples

# NOT RUN {
## Set options: opts_flow$set()
opts = opts_flow$set(flow_run_path = "~/mypath")
## OR if you would like to supply a long list of options:
opts = opts_flow$set(.dots = list(flow_run_path = "~/mypath"))

## load options from a configuration file: opts_flow$load()
conffile = fetch_conf("flowr.conf")
opts_flow$load(conffile)

## Fetch options: get_opts()
opts_flow$get("flow_run_path")
opts_flow$get()

# }