Add README files and disable generateSpec for all plugins

- Add README.md files for all plugins following the nextflow-plugin-gradle requirements
- Each README includes: Summary, Get Started, Examples, Resources, and License sections
- Disable generateSpec in build.gradle for all plugins (temporary workaround)

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

Author: pditommaso

plugins/gradle.properties

@@ -1,3 +1,3 @@
 ## plugins settings
-nextflowPluginVersion=1.0.0-beta.10
+nextflowPluginVersion=1.0.0-beta.11
 nextflowPluginProvider=nextflow-io

plugins/nf-amazon/README.md

@@ -0,0 +1,87 @@
+# Nextflow plugin for Amazon Web Services
+
+This plugin provides support for Amazon Web Services (AWS), including AWS Batch as a compute executor, S3 as a file system, and Fusion file system for high-performance data operations.
+
+## Get Started
+
+To use this plugin, add it to your `nextflow.config`:
+
+```groovy
+plugins {
+    id 'nf-amazon'
+}
+```
+
+Configure your AWS credentials using environment variables, AWS CLI profiles, or IAM roles. Then set up the executor and work directory:
+
+```groovy
+process.executor = 'awsbatch'
+process.queue = '<YOUR BATCH QUEUE>'
+workDir = 's3://<YOUR BUCKET>/work'
+
+aws {
+    region = 'us-east-1'
+    batch {
+        cliPath = '/home/ec2-user/miniconda/bin/aws'
+    }
+}
+```
+
+## Examples
+
+### Basic AWS Batch Configuration
+
+```groovy
+plugins {
+    id 'nf-amazon'
+}
+
+process.executor = 'awsbatch'
+process.queue = 'my-batch-queue'
+workDir = 's3://my-bucket/work'
+
+aws {
+    region = 'eu-west-1'
+    batch {
+        cliPath = '/home/ec2-user/miniconda/bin/aws'
+        jobRole = 'arn:aws:iam::123456789:role/MyBatchJobRole'
+    }
+}
+```
+
+### Using Fusion File System
+
+```groovy
+fusion {
+    enabled = true
+}
+
+wave {
+    enabled = true
+}
+
+process.executor = 'awsbatch'
+workDir = 's3://my-bucket/work'
+```
+
+### S3 Storage Options
+
+```groovy
+aws {
+    client {
+        maxConnections = 20
+        connectionTimeout = 10000
+        storageEncryption = 'AES256'
+    }
+    region = 'us-east-1'
+}
+```
+
+## Resources
+
+- [AWS Batch Executor Documentation](https://nextflow.io/docs/latest/aws.html)
+- [Amazon S3 Storage Documentation](https://nextflow.io/docs/latest/aws.html#s3-storage)
+
+## License
+
+[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0)

plugins/nf-amazon/build.gradle

@@ -25,6 +25,7 @@ nextflowPlugin {
     description = 'Provides comprehensive AWS cloud integration including Batch executor, S3 file system, and Fusion support for high-performance data operations'
     className = 'nextflow.cloud.aws.AmazonPlugin'
     useDefaultDependencies = false
+    generateSpec = false
     extensionPoints = [
         'nextflow.cloud.aws.batch.AwsBatchExecutor',
         'nextflow.cloud.aws.config.AwsConfig',

plugins/nf-azure/README.md

@@ -1,70 +1,83 @@
-# Azure plugin for Nextflow
+# Nextflow plugin for Microsoft Azure
 
-This plugin implements the support for Azure Blob storage as file system
-provider (via JSR203 interface) and Azure Batch executor for Nextflow.
+This plugin provides support for Azure Blob Storage as a file system and Azure Batch as a compute executor for Nextflow pipelines.
 
-## Development
+## Get Started
 
-Build Nextflow as usual:
+To use this plugin, add it to your `nextflow.config`:
 
-```bash
-make compile
+```groovy
+plugins {
+    id 'nf-azure'
+}
 ```
 
-Use the following Nextflow configuration:
+Configure your Azure credentials and services:
+
+```groovy
+azure {
+    storage {
+        accountName = '<YOUR STORAGE ACCOUNT NAME>'
+        accountKey = '<YOUR STORAGE ACCOUNT KEY>'
+    }
+
+    batch {
+        endpoint = 'https://<YOUR BATCH ACCOUNT NAME>.<REGION>.batch.azure.com'
+        accountName = '<YOUR BATCH ACCOUNT NAME>'
+        accountKey = '<YOUR BATCH ACCOUNT KEY>'
+    }
+}
+```
+
+Set the executor and work directory:
+
+```groovy
+process.executor = 'azurebatch'
+workDir = 'az://<YOUR CONTAINER>/work'
+```
+
+## Examples
+
+### Basic Azure Batch Configuration
 
 ```groovy
 plugins {
-  id 'nf-azure'
+    id 'nf-azure'
 }
 
 azure {
-  storage {
-    accountKey = "<YOUR STORAGE ACCOUNT KEY>"
-    accountName = "<YOUR STORAGE ACCOUNT KEY>"
-  }
-
-  batch {
-    endpoint = 'https://<YOUR BATCH ACCOUNT NAME>.westeurope.batch.azure.com'
-    accountName = '<YOUR BATCH ACCOUNT NAME>'
-    accountKey = '<YOUR BATCH ACCOUNT KEY>'
-  }
+    storage {
+        accountName = 'mystorageaccount'
+        accountKey = System.getenv('AZURE_STORAGE_KEY')
+    }
+
+    batch {
+        endpoint = 'https://mybatchaccount.westeurope.batch.azure.com'
+        accountName = 'mybatchaccount'
+        accountKey = System.getenv('AZURE_BATCH_KEY')
+        autoPoolMode = true
+        deletePoolsOnCompletion = true
+    }
 }
 
 process.executor = 'azurebatch'
-workDir = 'az://<YOUR DATA CONTAINER>/work'
+workDir = 'az://mycontainer/work'
 ```
 
-Then test the local build as usual:
+### Using Managed Identity
 
-```bash
-./launch.sh run -c nextflow.config rnaseq-nf
+```groovy
+azure {
+    managedIdentity {
+        clientId = '<YOUR MANAGED IDENTITY CLIENT ID>'
+    }
+}
 ```
 
-## Todo
-
-* Currently, the Blob storage service uses NettyHttpClient and Batch service
-  uses OkHttp client, duplicating the number of required libraries. In principle
-  the Blob service can use OkHttp, adding the following deps, however using that
-  Nextflow hangs during the shutdown, apparently because the connection pool used
-  by the blob service is not closed timely.
-
-  ```groovy
-  compile('com.azure:azure-storage-blob:12.9.0') {
-      exclude group: 'org.slf4j', module: 'slf4j-api'
-      exclude group: 'com.azure', module: 'azure-core-http-netty'
-  }
-  compile('com.azure:azure-core-http-okhttp:1.3.3') {
-      exclude group: 'org.slf4j', module: 'slf4j-api'
-  }
-  ```
-
-* Remove invalid directory from .command.run PATH for project having `bin/` folder
-* Add the configuration for the region
-* Make the backend endpoint optional
-
-### Additional Resources
-
-* https://github.com/Azure/azure-sdk-for-java/wiki
-* https://github.com/Azure/azure-sdk-for-java/tree/master/sdk/storage/azure-storage-blob-nio
-* https://github.com/Azure/azure-sdk-for-java/blob/master/sdk/storage/azure-storage-blob-nio/src/samples/java/com/azure/storage/blob/nio/ReadmeSamples.java
+## Resources
+
+- [Azure Batch Executor Documentation](https://nextflow.io/docs/latest/azure.html)
+
+## License
+
+[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0)

plugins/nf-azure/build.gradle

@@ -25,6 +25,7 @@ nextflowPlugin {
     description = 'Enables Azure cloud execution through Batch service with native Blob storage access and comprehensive authentication options'
     className = 'nextflow.cloud.azure.AzurePlugin'
     useDefaultDependencies = false
+    generateSpec = false
     extensionPoints = [
         'nextflow.cloud.azure.batch.AzBatchExecutor',
         'nextflow.cloud.azure.config.AzConfig',

plugins/nf-cloudcache/README.md

@@ -0,0 +1,84 @@
+# Nextflow plugin for cloud cache
+
+This plugin provides cloud-based caching support for Nextflow pipelines, enabling workflow resume capability when using cloud storage as the work directory.
+
+## Get Started
+
+To use this plugin, add it to your `nextflow.config`:
+
+```groovy
+plugins {
+    id 'nf-cloudcache'
+}
+```
+
+The plugin is automatically activated when using cloud storage (S3, GS, Azure Blob) as the work directory with resume enabled.
+
+```groovy
+workDir = 's3://my-bucket/work'
+```
+
+Run your pipeline with the `-resume` flag:
+
+```bash
+nextflow run main.nf -resume
+```
+
+## Examples
+
+### AWS S3 Cache
+
+```groovy
+plugins {
+    id 'nf-amazon'
+    id 'nf-cloudcache'
+}
+
+workDir = 's3://my-bucket/work'
+
+aws {
+    region = 'us-east-1'
+}
+```
+
+### Google Cloud Storage Cache
+
+```groovy
+plugins {
+    id 'nf-google'
+    id 'nf-cloudcache'
+}
+
+workDir = 'gs://my-bucket/work'
+
+google {
+    project = 'my-project'
+    location = 'us-central1'
+}
+```
+
+### Azure Blob Storage Cache
+
+```groovy
+plugins {
+    id 'nf-azure'
+    id 'nf-cloudcache'
+}
+
+workDir = 'az://my-container/work'
+
+azure {
+    storage {
+        accountName = 'mystorageaccount'
+        accountKey = System.getenv('AZURE_STORAGE_KEY')
+    }
+}
+```
+
+## Resources
+
+- [Nextflow Cache and Resume](https://nextflow.io/docs/latest/cache-and-resume.html)
+
+## License
+
+[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0)

plugins/nf-cloudcache/build.gradle

@@ -25,6 +25,7 @@ nextflowPlugin {
     description = 'Implements cloud-based caching system to optimize workflow performance by reducing redundant computations and data transfers'
     className = 'nextflow.CloudCachePlugin'
     useDefaultDependencies = false
+    generateSpec = false
     extensionPoints = [
         'nextflow.cache.CloudCacheFactory'
     ]