nf-modules

Reusable modules and subworkflows for Nextflow pipelines

Usage

To re-use a module in your nextflow pipeline, first install nf-core tools, then run

nf-core modules \
  --git-remote https://github.com/CCBR/nf-modules \
  install [module]

replacing [module] with the name of the module you wish to install.

To update your local version of a module, run

nf-core modules \
  --git-remote https://github.com/CCBR/nf-modules \
  update [module]

Use the subworkflows command in place of the modules command to install or update subworkflows.

nf-core subworkflows \
  --git-remote https://github.com/CCBR/nf-modules \
  update [subworkflow]

Help & Contributing

Come across a bug? Open an issue and include a minimal reproducible example.

Have a question? Ask it in discussions.

Want to contribute to this project? Check out the contributing guidelines.

References

Many of the modules and subworkflows in this project reuse and adapt code from nf-core/modules. In those cases, credit is noted in the meta.yml file of the module/subworkflow and also listed here:

• bedtools adapts the nf-core bedtools module
• bwa adapts the nf-core bwa module
• cat adapts the nf-core cat module
• cutadapt adapts the nf-core cutadapt module
• khmer adapts the nf-core khmer module
• picard/samtofastq adapts the nf-core gatk4 samtofastq module
• samtools/sort adapts the nf-core samtools sort module