R: Default options/params used in flowr and ngsflows

flowopts {flowr} | R Documentation

## 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 seperated text file

For more details regarding these funtions 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 seperated by commas

### Format

`opts_flow`

### 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

    ## 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()

[Package flowr version 0.9.10 Index]