nf-core/configs: GA4GH TES Configuration

To be used with the tes profile by specifying the -profile tes when running nf-core pipelines. Custom endpoints and authentication need to be supplied with params.endpoint, params.basicUsername, params.basicPassword. Additionally you will need to add the -plugin nf-ga4gh at command line to import the correct plugin.

Required Parameters

--endpoint

URL of TES endpoint.

--basicUsername

Username for authentication for TES endpoint.

--basicPassword

Password for authentication for TES endpoint.

Config file

See config file on GitHub

conf/tes
//Nextflow config file for running on TES Backend
process {
    executor = "tes"
}
 
params {
    config_profile_description = 'GA4GH TES Profile'
    config_profile_contact     = 'Venkat Malladi (@vsmalladi)'
    config_profile_url         = 'https://github.com/ga4gh/task-execution-schemas'
 
    // TES
    endpoint                   = null
    basicUsername              = null
    basicPassword              = null
}
 
tes {
    endpoint        = params.endpoint
    basicUsername   = params.basicUsername
    basicPassword   = params.basicPassword
}
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