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.
Note

You can use the meta.yml file to specify different remotes for the components in your subworkflow. This is useful when you want to use modules from organisations different from the one where the subworkflow is located. For more information, see our tutorial.