https://github.com/midnighter/nextflow-utility-services

A collection of Groovy classes that provide utility services to nextflow pipelines.
https://github.com/midnighter/nextflow-utility-services

Last synced: 11 days ago
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A collection of Groovy classes that provide utility services to nextflow pipelines.

• Host: GitHub
• URL: https://github.com/midnighter/nextflow-utility-services
• Owner: Midnighter
• License: mit
• Created: 2022-09-19T18:45:48.000Z (about 2 years ago)
• Default Branch: main
• Last Pushed: 2022-10-25T05:56:39.000Z (about 2 years ago)
• Last Synced: 2024-04-16T03:31:29.748Z (7 months ago)
• Language: Groovy
• Size: 33.2 KB
• Stars: 13
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Nextflow Utility Services

A collection of custom Groovy service classes intended for use in nextflow pipelines.

| Service                                                                                                                                             | Demo                                        | Description                                                                                              |

| --------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------- | -------------------------------------------------------------------------------------------------------- |

| [`lib/FormattingService.groovy`](lib/FormattingService.groovy)                                                                                      | `nextflow run formatting.nf -dump-channels` | Format objects as JSON for pretty printing.                                                              |

| [`lib/FileTypeQueryService.groovy`](lib/FileTypeQueryService.groovy)                                                                                | `nextflow run file_type_query.nf`           | Query file path objects for compression and common sequencing data types. Can be extended indefinitely.  |

| [`lib/CustomChannelOperators.groovy`](lib/CustomChannelOperators.groovy)                                                                            | `nextflow run join_on_keys.nf`              | Extract values via given keys from maps in two different channels and join those channels on the values. |

| [`lib/HTTPRequestsService.groovy`](lib/HTTPRequestsService.groovy)
[`lib/HTTPResponse.groovy`](lib/HTTPResponse.groovy)                         | `nextflow run http_requests.nf`             | Perform HTTP requests via a simplified API. At the moment only POST is supported.                        |

| [`lib/SlackMessagingService.groovy`](lib/SlackMessagingService.groovy)
[`assets/pipelineStatusMessage.json`](assets/pipelineStatusMessage.json) | `nextflow run slack_messaging.nf`           | Post a pipeline status message to Slack using an incoming webhook URL.                                   |

## Usage

If you intend to use one or more of the classes from this repository. Simply copy them from the [`lib`](lib) directory to your pipeline's `lib` directory. Some classes additionally require assets which you should similarly copy from the [`assets`](assets) directory to your pipeline's `assets` directory.

If you want to use a service inside one of your modules, rather than in the main workflow, you may have to import it by its class name.

```nextflow

import Service

```

## Copyright

-   Copyright © 2022, Moritz E. Beber

-   Free software, distributed under the [MIT license](LICENSE)