https://github.com/munishchouhan/nf-test-pipeline

nextflow pipeline for test
https://github.com/munishchouhan/nf-test-pipeline

Last synced: about 2 months ago
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nextflow pipeline for test

• Host: GitHub
• URL: https://github.com/munishchouhan/nf-test-pipeline
• Owner: munishchouhan
• Created: 2023-10-02T10:16:57.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2024-04-16T11:41:07.000Z (9 months ago)
• Last Synced: 2024-04-16T14:41:45.705Z (9 months ago)
• Language: Nextflow
• Size: 5.86 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# Build and deliver Nextflow module containers

### Summary 

This example shows how to associate a Dockerfile with a Nextflow module.

When executing a pipeline script enabling the Wave plugin, the Dockerfile 

is uploaded to the Wave service, a container is built on-the-fly, and pushed to

a temporary repository. The container name is automatically included in the 

process execution and used to run the task.

### Pipeline script 

The pipeline script includes a simple module and uses it in the workflow:

```nextflow

include { hello } from './modules/foo'

workflow {

  hello()

}

```

### Module script 

```nextflow

process hello {

  debug true

  """

  cowsay Hello Summit! 

  """

}

```

Note: the process does not need to declare any `container` to used. Instead, a `Dockerfile` is included in the module directory.

### Dockerfile 

The Dockerfile defines the software to be installed.

```Dockerfile

FROM alpine 

RUN apk update && apk add bash cowsay \

        --update-cache \

        --repository https://alpine.global.ssl.fastly.net/alpine/edge/community \

        --repository https://alpine.global.ssl.fastly.net/alpine/edge/main \

        --repository https://dl-3.alpinelinux.org/alpine/edge/testing

```

### Run it 

```bash

nextflow run main.nf -with-wave

```