Install a subworkflow

You can install subworkflows from nf-core/modules in your pipeline using nf-core subworkflows install. A subworkflow installed this way will be installed to the ./subworkflows/nf-core directory.

nf-core subworkflows install bam_rseqc

You can pass the subworkflow name as an optional argument to nf-core subworkflows install like above or select it from a list of available subworkflows by only running nf-core subworkflows install.

There are four additional flags that you can use when installing a subworkflow:

  • --dir: Pipeline directory, the default is the current working directory.
  • --force: Overwrite a previously installed version of the subworkflow.
  • --prompt: Select the subworkflow version using a cli prompt.
  • --sha <commit_sha>: Install the subworkflow at a specific commit.