Remove GA4GH plugin (#5056)

Signed-off-by: Paolo Di Tommaso <[email protected]>

Makefile

@@ -100,12 +100,6 @@ pack:
 packCore:
 	BUILD_PACK=1 ./gradlew packCore
 
-#
-# Create self-contained distribution package, including GA4GH support and associated dependencies
-#
-packGA4GH:
-	BUILD_PACK=1 ./gradlew -PGA4GH packAll
-
 #
 # Upload NF launcher to nextflow.io web site
 #

docs/executor.md

@@ -114,68 +114,6 @@ Flux does not support the `memory` directive.
 By default, Flux will send all output to the `.command.log` file. To send this output to stdout and stderr instead, set `flux.terminalOutput = true` in your config file.
 :::
 
-(ga4ghtes-executor)=
-
-## GA4GH TES
-
-:::{warning} *Experimental: may change in a future release.*
-:::
-
-:::{versionchanged} 23.07.0-edge
-Support for automatic upload of the `bin` directory was added.
-:::
-
-:::{versionchanged} 24.04.0
-Support for process output directories and output globs was added.
-:::
-
-The [Task Execution Schema](https://github.com/ga4gh/task-execution-schemas) (TES) project by the [GA4GH](https://www.ga4gh.org) standardization initiative is an effort to define a standardized schema and API for describing batch execution tasks in a portable manner.
-
-Nextflow supports the TES API via the `tes` executor, which allows the submission of workflow tasks to a remote execution backend exposing a TES API endpoint.
-
-The pipeline processes must specify the Docker image to use by defining the `container` directive, either in the pipeline script or the `nextflow.config` file. Additionally, the pipeline work directory must be accessible to the TES backend.
-
-To enable this executor, add the following settings to your Nextflow configuration:
-
-```groovy
-plugins {
-  id 'nf-ga4gh'
-}
-
-process.executor = 'tes'
-tes.endpoint = '<endpoint>'
-```
-
-The default endpoint is `http://localhost:8000`. It is important that the endpoint is specified without the trailing slash; otherwise, the resulting URLs will not be normalized and the requests to TES will fail.
-
-The TES API supports multiple forms of authentication:
-
-```groovy
-// basic
-tes.basicUsername = '<username>'
-tes.basicPassword = '<password>'
-
-// API key
-tes.apiKeyParamMode = '<mode>' // 'query' or 'header'
-tes.apiKeyParamName = '<param-name>'
-tes.apiKey = '<key>'
-
-// OAuth
-tes.oauthToken = '<token>'
-```
-
-:::{tip}
-You can deploy a local [Funnel](https://ohsu-comp-bio.github.io/funnel/) server using the following command:
-
-```bash
-./funnel server --Server.HTTPPort 8000 --LocalStorage.AllowedDirs $HOME run
-```
-:::
-
-:::{note}
-While the TES API is designed to abstract workflow managers from direct storage access, Nextflow still needs to access the shared work directory used by your TES endpoint. For example, if your TES endpoint is located in Azure and uses Azure Blob storage to store the work directory, you still need to provide the necessary Azure credentials for Nextflow to access the Blob storage.
-:::
-
 (google-batch-executor)=
 
 ## Google Cloud Batch

docs/plugins.md

@@ -14,7 +14,6 @@ The following functionalities are provided via plugin components, and they make
 - `nf-azure`: Support for Microsoft Azure.
 - `nf-cloudcache`: Support for the cloud cache (see `NXF_CLOUDCACHE_PATH` under {ref}`config-env-vars`).
 - `nf-console`: Implement Nextflow [REPL console](https://www.nextflow.io/blog/2015/introducing-nextflow-console.html).
-- `nf-ga4gh`: Support [GA4GH APIs](https://www.ga4gh.org/).
 - `nf-google`: Support for Google Cloud.
 - `nf-tower`: Support for [Seqera Platform](https://seqera.io) (formerly Tower Cloud).
 - `nf-wave`: Support for [Wave containers](https://seqera.io/wave/) service.

docs/process.md

@@ -1725,7 +1725,6 @@ The following executors are available:
 | `pbspro`              | [PBS Pro](https://www.pbsworks.com/) job scheduler                                          |
 | `sge`                 | Sun Grid Engine / [Open Grid Engine](http://gridscheduler.sourceforge.net/)                 |
 | `slurm`               | [SLURM](https://en.wikipedia.org/wiki/Slurm_Workload_Manager) workload manager              |
-| `tes`                 | [GA4GH TES](https://github.com/ga4gh/task-execution-schemas) service                        |
 | `uge`                 | Alias for the `sge` executor                                                                |
 
 The following example shows how to set the process's executor:

packing.gradle

@@ -3,7 +3,6 @@ configurations {
     defaultCfg.extendsFrom api 
     //provided
     console.extendsFrom defaultCfg
-    ga4gh.extendsFrom defaultCfg
     google.extendsFrom defaultCfg
     amazon.extendsFrom defaultCfg
     azure.extendsFrom defaultCfg
@@ -22,7 +21,6 @@ dependencies {
     capsule 'io.nextflow:capsule:1.1.1'
     capsule 'io.nextflow:capsule-maven:1.0.3.2'
     console project(':plugins:nf-console')
-    ga4gh   project(':plugins:nf-ga4gh')
     google  project(':plugins:nf-google')
     amazon  project(':plugins:nf-amazon')
     azure   project(':plugins:nf-azure')
@@ -150,12 +148,6 @@ task packAll(type: Jar) {
     manifest.attributes('Main-Class': 'NextflowLoader', 'amazon')
     manifest.attributes('Main-Class': 'NextflowLoader', 'google')
 
-    if( project.hasProperty('GA4GH') ) {
-        println "The build will include GA4GH dependencies."
-        from(configurations.ga4gh)
-        manifest.attributes('Main-Class': 'CapsuleLoader', 'ga4gh')
-    }
-
     doLast {
         file(releaseDir).mkdir()
         // cleanup