Add README files for all plugins #6660

pditommaso · 2025-12-13T13:06:00Z

Summary

Add README.md files for all 9 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

Changes

New README files

plugins/nf-amazon/README.md
plugins/nf-azure/README.md (updated)
plugins/nf-cloudcache/README.md
plugins/nf-codecommit/README.md
plugins/nf-console/README.md
plugins/nf-google/README.md
plugins/nf-k8s/README.md
plugins/nf-tower/README.md
plugins/nf-wave/README.md

Build configuration

Added generateSpec = false to all plugin build.gradle files

Test plan

Verify README files are correctly formatted
Run ./gradlew releasePluginToRegistryIfNotExists to verify plugin release works

🤖 Generated with Claude Code

netlify · 2025-12-13T13:06:05Z

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- 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]>

christopher-hakkaart

I've added some suggestions to name the plugin in the first sentence to improve clarity, but otherwise looks good.

plugins/nf-amazon/README.md

plugins/nf-azure/README.md

plugins/nf-cloudcache/README.md

plugins/nf-codecommit/README.md

plugins/nf-console/README.md

plugins/nf-google/README.md

plugins/nf-k8s/README.md

plugins/nf-tower/README.md

plugins/nf-wave/README.md

Co-authored-by: Chris Hakkaart <[email protected]> Signed-off-by: Paolo Di Tommaso <[email protected]>

pditommaso · 2025-12-15T08:16:56Z

Awesome thanks

bentsherman · 2025-12-15T14:29:26Z

plugins/nf-amazon/README.md

+To use this plugin, add it to your `nextflow.config`:
+
+```groovy
+plugins {
+    id 'nf-amazon'
+}
+```


This seems unnecessary since core plugins are enabled automatically

Same for all the other READMEs

That's true, however it may be better to keep for consistency with plugin config syntax

plugins/gradle.properties

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

christopher-hakkaart

I've added suggestions to change the headings into sentence case, which we use for regular documentation.

christopher-hakkaart · 2025-12-17T00:29:13Z

docs/guides/gradle-plugin.md

+1. **Summary** - Explain what the plugin does
+2. **Get Started** - Setup and configuration instructions
+3. **Examples** - Code examples with code blocks
+4. **License** - Specify the plugin's license (e.g., Apache 2.0, MIT, GPL)


Suggested change

1. **Summary** - Explain what the plugin does

2. **Get Started** - Setup and configuration instructions

3. **Examples** - Code examples with code blocks

4. **License** - Specify the plugin's license (e.g., Apache 2.0, MIT, GPL)

1. **Summary:** Explain what the plugin does

2. **Get started:** Setup and configuration instructions

3. **Examples:** Provide code examples with code blocks

4. **License:** Specify the plugin's license (e.g., Apache 2.0, MIT, GPL)

I haven't checked the code, but will these headings be tested/checked for in PRs?

If so, are the headings case sensitive? Are there requirements for their level (e.g., H2 or H3)?

christopher-hakkaart · 2025-12-17T00:34:08Z

plugins/nf-amazon/README.md

+
+The Amazon Web Services (AWS) plugin provides support for AWS, including AWS Batch as a compute executor, S3 as a file system, and Fusion file system for high-performance data operations.
+
+## Get Started


Suggested change

## Get Started

## Get started

christopher-hakkaart · 2025-12-17T00:34:21Z

plugins/nf-amazon/README.md

+
+## Examples
+
+### Basic AWS Batch Configuration


Suggested change

### Basic AWS Batch Configuration

### Basic AWS Batch configuration

christopher-hakkaart · 2025-12-17T00:34:49Z

plugins/nf-amazon/README.md

+}
+```
+
+### Using Fusion File System


Suggested change

### Using Fusion File System

### Using Fusion file system

christopher-hakkaart · 2025-12-17T00:34:59Z

plugins/nf-amazon/README.md

+workDir = 's3://my-bucket/work'
+```
+
+### S3 Storage Options


Suggested change

### S3 Storage Options

### S3 storage options

christopher-hakkaart · 2025-12-17T00:42:18Z

plugins/nf-tower/README.md

+}
+```
+
+### Reports and Cache Management


Suggested change

### Reports and Cache Management

### Reports and cache management

christopher-hakkaart · 2025-12-17T00:42:32Z

plugins/nf-wave/README.md

+
+The Wave containers plugin provides integration with the Wave container service for dynamic container building, augmentation, and on-demand software provisioning.
+
+## Get Started


Suggested change

## Get Started

## Get started

christopher-hakkaart · 2025-12-17T00:42:55Z

plugins/nf-wave/README.md

+### Basic Wave Configuration
+
+```groovy
+plugins {
+    id 'nf-wave'
+}
+
+wave {
+    enabled = true
+}
+
+process {
+    conda = 'samtools=1.17'
+}
+```
+
+### Using Wave with Conda Packages


Suggested change

### Basic Wave Configuration

```groovy

plugins {

id 'nf-wave'

}

wave {

enabled = true

}

process {

conda = 'samtools=1.17'

}

```

### Using Wave with Conda Packages

### Basic Wave configuration

```groovy

plugins {

id 'nf-wave'

}

wave {

enabled = true

}

process {

conda = 'samtools=1.17'

}

```

### Using Wave with Conda packages

christopher-hakkaart · 2025-12-17T00:43:09Z

plugins/nf-wave/README.md

+}
+```
+
+### Wave with Fusion File System


Suggested change

### Wave with Fusion File System

### Wave with Fusion file system

christopher-hakkaart · 2025-12-17T00:43:54Z

plugins/nf-wave/README.md

+### Container Augmentation
+
+```groovy
+wave {
+    enabled = true
+    strategy = 'conda,container'
+}
+
+process TOOL {
+    container 'ubuntu:22.04'
+    conda 'bioconda::samtools=1.17'
+
+    script:
+    '''
+    samtools --version
+    '''
+}
+```
+
+### Using Private Registries


Suggested change

### Container Augmentation

```groovy

wave {

enabled = true

strategy = 'conda,container'

}

process TOOL {

container 'ubuntu:22.04'

conda 'bioconda::samtools=1.17'

script:

'''

samtools --version

'''

}

```

### Using Private Registries

### Container augmentation

```groovy

wave {

enabled = true

strategy = 'conda,container'

}

process TOOL {

container 'ubuntu:22.04'

conda 'bioconda::samtools=1.17'

script:

'''

samtools --version

'''

}

```

### Using private registries

christopher-hakkaart

I've added suggestions to change the headings into sentence case, which we use for regular documentation.

pditommaso requested a review from christopher-hakkaart December 13, 2025 13:06

pditommaso force-pushed the add-plugin-readmes branch from e364d8f to 17f04b9 Compare December 13, 2025 13:10

pditommaso force-pushed the add-plugin-readmes branch from 17f04b9 to fd27493 Compare December 13, 2025 13:13

christopher-hakkaart approved these changes Dec 14, 2025

View reviewed changes

pditommaso and others added 9 commits December 15, 2025 09:15

Update plugins/nf-amazon/README.md [ci skip]

86afc68

Co-authored-by: Chris Hakkaart <[email protected]> Signed-off-by: Paolo Di Tommaso <[email protected]>

Update plugins/nf-azure/README.md [ci skip]

e5641c5

Co-authored-by: Chris Hakkaart <[email protected]> Signed-off-by: Paolo Di Tommaso <[email protected]>

Update plugins/nf-cloudcache/README.md [ci skip]

32f9bda

Co-authored-by: Chris Hakkaart <[email protected]> Signed-off-by: Paolo Di Tommaso <[email protected]>

Update plugins/nf-codecommit/README.md [ci skip]

357fdfb

Co-authored-by: Chris Hakkaart <[email protected]> Signed-off-by: Paolo Di Tommaso <[email protected]>

Update plugins/nf-console/README.md [ci skip]

059eb0b

Co-authored-by: Chris Hakkaart <[email protected]> Signed-off-by: Paolo Di Tommaso <[email protected]>

Update plugins/nf-google/README.md [ci skip]

1e5ad23

Co-authored-by: Chris Hakkaart <[email protected]> Signed-off-by: Paolo Di Tommaso <[email protected]>

Update plugins/nf-k8s/README.md [ci skip]

fadb59f

Co-authored-by: Chris Hakkaart <[email protected]> Signed-off-by: Paolo Di Tommaso <[email protected]>

Update plugins/nf-tower/README.md [ci skip]

2b0bb05

Co-authored-by: Chris Hakkaart <[email protected]> Signed-off-by: Paolo Di Tommaso <[email protected]>

Update plugins/nf-wave/README.md [ci skip]

73c0c0d

Co-authored-by: Chris Hakkaart <[email protected]> Signed-off-by: Paolo Di Tommaso <[email protected]>

bentsherman reviewed Dec 15, 2025

View reviewed changes

pditommaso commented Dec 16, 2025

View reviewed changes

plugins/gradle.properties Outdated Show resolved Hide resolved

pditommaso added 3 commits December 16, 2025 17:39

Update plugins/gradle.properties [ci fast]

305d850

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

Fix failing tests [ci fast]

ebfa0de

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

Update docs [ci skip]

8382c67

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

pditommaso requested a review from a team as a code owner December 16, 2025 17:56

Merge branch 'master' into add-plugin-readmes

72aa88c

christopher-hakkaart reviewed Dec 17, 2025

View reviewed changes


		The Amazon Web Services (AWS) plugin provides support for AWS, including AWS Batch as a compute executor, S3 as a file system, and Fusion file system for high-performance data operations.

		## Get Started

	### Basic AWS Batch Configuration
	### Basic AWS Batch configuration

	### Reports and Cache Management
	### Reports and cache management


		The Wave containers plugin provides integration with the Wave container service for dynamic container building, augmentation, and on-demand software provisioning.

		## Get Started

	### Wave with Fusion File System
	### Wave with Fusion file system

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Summary

Changes

New README files

Build configuration

Test plan

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✅ Deploy Preview for nextflow-docs-staging ready!

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pditommaso commented Dec 15, 2025

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pditommaso commented Dec 13, 2025 •

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