nf-core / modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
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Repository Overview (README excerpt)
Crawler viewA repository for hosting Nextflow DSL2 module files containing tool-specific process definitions and their associated documentation. Table of contents • Using existing modules • Adding new modules • Help • Citation Using existing modules The module files hosted in this repository define a set of processes for software tools such as , , etc. This allows you to share and add common functionality across multiple pipelines in a modular fashion. We have written a helper command in the package that uses the GitHub API to obtain the relevant information for the module files present in the directory of this repository. This includes using commit hashes to track changes for reproducibility purposes, and to download and install all of the relevant module files. • Install the latest version of ( ) • List the available modules: • Install the module in your pipeline directory: • Import the module in your Nextflow script: • Remove the module from the pipeline repository if required: • Check that a locally installed nf-core module is up-to-date compared to the one hosted in this repo: Adding new modules If you wish to contribute a new module, please see the documentation on the nf-core website. > Please be kind to our code reviewers and submit one pull request per module :) Help For further information or help, don't hesitate to get in touch on Slack channel (you can join with this invite). Citation If you use the module files in this repository for your analysis please you can cite the publication as follows: > **The nf-core framework for community-curated bioinformatics pipelines.** > > Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. > > _Nat Biotechnol._ 2020 Feb 13. doi: 10.1038/s41587-020-0439-x. Note that the nf-core/tools helper package has a command to download all required pipeline > files + singularity containers + institutional configs + modules in one go for you, to make this process easier. New test data created for the module- sequenzautils/bam2seqz The new test data is an output from another module- sequenzautils/bcwiggle- (which uses sarscov2 genome fasta file as an input). --> CI Runners We are using self-hosted runners for the CI tests, managed via RunsOn.