Merge branch 'master' into batch-resourcelimit-update

.github/workflows/main.yml

@@ -134,6 +134,7 @@ jobs:
           - "self_hosted_runner"
           - "seg_globe"
           - "software_license"
+          - "tes"
           - "tigem"
           - "tubingen_apg"
           - "tufts"

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)

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
+}
+
+

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.

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"
     }