Welcome to the Microbiome Informatics Nextflow modules and subworkflows repository. This repository uses the same tools and conventions as nf-core modules.

To use the modules and subworkflows from this repository make sure you have nf-core/tools installed:

pip install nf-core

List the available modules:

nf-core modules --git-remote [email protected]:EBI-Metagenomics/nf-modules.git list remote

Install a module in your pipeline:

nf-core modules --git-remote [email protected]:EBI-Metagenomics/nf-modules.git install <tool>

Then import the desired module in your pipeline script:

include { module_name } from '../modules/ebi-metagenomics/tool/main.nf'

Subworkflows in this repository are self-contained and can be included in your main pipeline:

Install a module in your pipeline:

nf-core subworkflows --git-remote [email protected]:EBI-Metagenomics/nf-modules.git install <subworkflow>

Then import the desired module in your pipeline script:

include { <subworkflow_name> } from '../subworkflows/ebi-metagenomics/<subworkflow_name>.nf'

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

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.