Reusable modules and subworkflows for Nextflow pipelines
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]
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.
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