diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index e8f77cbd..ba8799dc 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -134,6 +134,7 @@ jobs: - "self_hosted_runner" - "seg_globe" - "software_license" + - "tes" - "tigem" - "tubingen_apg" - "tufts" diff --git a/README.md b/README.md index 9a35cbe4..c52a8c68 100644 --- a/README.md +++ b/README.md @@ -184,6 +184,7 @@ Currently documentation is available for the following systems: - [SEG_GLOBE](docs/seg_globe.md) - [self-hosted-runner](docs/self-hosted-runner.md) - [Super Computing Wales](docs/scw.md) +- [GA4GH TES](docs/tes.md) - [TIGEM](docs/tigem.md) - [TUBINGEN_APG](docs/tubingen_apg.md) - [TUFTS](docs/tufts.md) diff --git a/conf/tes.config b/conf/tes.config new file mode 100644 index 00000000..88d44de1 --- /dev/null +++ b/conf/tes.config @@ -0,0 +1,23 @@ +//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 +} + + diff --git a/docs/tes.md b/docs/tes.md new file mode 100644 index 00000000..b6f543bf --- /dev/null +++ b/docs/tes.md @@ -0,0 +1,19 @@ +# 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. diff --git a/nfcore_custom.config b/nfcore_custom.config index 8b265e50..d4ed7761 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -313,6 +313,9 @@ profiles { software_license { includeConfig "${params.custom_config_base}/conf/software_license.config" } + tes { + includeConfig "${params.custom_config_base}/conf/tes.config" + } tigem { includeConfig "${params.custom_config_base}/conf/tigem.config" }