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Repository to host tool-specific module files for the Nextflow DSL2 community!
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README.md

nf-core/modules

DSL2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT. SYNTAX, ORGANISATION AND LAYOUT OF THIS REPOSITORY MAY CHANGE IN THE NEAR FUTURE!

A repository for hosting nextflow DSL2 module files and subworkflows containing tool-specific process definitions and their associated documentation.

Table of contents

Terminology

The DSLv2 features for Nextflow are new for everyone and not just beginners. We discussed some terminology terms to discuss things related to modules & subworkflows more appropriately:

  • Module: A processthat can be used between different pipelines, which is atomic (i.e. can/should not be divided further).
  • Subworkflow: A combined set of modules, that combine a logical step in a pipeline using multiple modules together. Example: A preprocessing subworkflow for FastQ input, that could be (re-) used across multiple pipelines to QC input FastQ files.
  • Workflow: What DSLv1 users would consider a pipeline, e.g. from input to potentially complex output. Can either consist of individual modules, a large monolithic script as in DSLv1 or a combination of subworkflows (or any combination of these three).

Organization of repository

  • Modules should end up in the subdirectory tools
  • Subworkflows should be kept with individual pipelines, and not end up here in the modules repository.

Using existing modules

The Nextflow include statement can be used within your pipelines in order to load module files that you have available locally.

You should be able to get a good idea as to how other people are using module files by looking at pipelines available in nf-core e.g. nf-core/rnaseq

Configuration and parameters

The module files hosted in this repository define a set of processes for software tools such as fastqc, trimgalore, bwa etc. This allows you to share and add common functionality across multiple pipelines in a modular fashion.

The definition and standards for module files are still under discussion amongst the community but hopefully, a description should be added here soon!

Offline usage

If you want to use an existing module file available in nf-core/modules, and you're running on a system that has no internet connection, you'll need to download the repository (e.g. git clone https://github.com/nf-core/modules.git) and place it in a location that is visible to the file system on which you are running the pipeline. Then run the pipeline by creating a custom config file called e.g. custom_module.conf containing the following information:

include /path/to/downloaded/modules/directory/

Then you can run the pipeline by directly passing the additional config file with the -c parameter:

nextflow run /path/to/pipeline/ -c /path/to/custom_module.conf

Note that the nf-core/tools helper package has a download command to download all required pipeline files + singularity containers + institutional configs + modules in one go for you, to make this process easier.

Adding a new module file

If you decide to upload your module file to nf-core/modules then this will ensure that it will be automatically downloaded, and available at run-time to all nf-core pipelines, and to everyone within the Nextflow community! See nf-core/modules/nf for examples.

The definition and standards for module files are still under discussion amongst the community but hopefully, a description should be added here soon!

Testing

If you want to add a new module config file to nf-core/modules please test that your pipeline of choice runs as expected by using the -include statement with a local version of the module file.

Documentation

Please add some documentation to the top of the module file in the form of native Nextflow comments. This has to be specified in a particular format as you will be able to see from other examples in the nf-core/modules/nf directory.

Uploading to nf-core/modules

Fork the nf-core/modules repository to your own GitHub account. Within the local clone of your fork add the module file to the nf-core/modules/nf directory. Please keep the naming consistent between the module and documentation files e.g. bwa.nf and bwa.md, respectively.

Commit and push these changes to your local clone on GitHub, and then create a pull request on nf-core/modules GitHub repo with the appropriate information.

We will be notified automatically when you have created your pull request, and providing that everything adheres to nf-core guidelines we will endeavour to approve your pull request as soon as possible.

Help

If you have any questions or issues please send us a message on Slack.