Update subworkflows

You can update subworkflows installed from a remote repository in your pipeline using nf-core subworkflows update.

nf-core subworkflows update --all --no-preview

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

There are six additional flags that you can use with this command:

  • --dir: Pipeline directory, the default is the current working directory.
  • --force: Reinstall subworkflow even if it appears to be up to date
  • --prompt: Select the subworkflow version using a cli prompt.
  • --sha <commit_sha>: Install the subworkflow at a specific commit from the nf-core/modules repository.
  • --preview/--no-preview: Show the diff between the installed files and the new version before installing.
  • --save-diff <filename>: Save diffs to a file instead of updating in place. The diffs can then be applied with git apply <filename>.
  • --all: Use this flag to run the command on all subworkflows in the pipeline.
  • --update-deps: Use this flag to automatically update all dependencies of a subworkflow.

If you don’t want to update certain subworkflows or want to update them to specific versions, you can make use of the .nf-core.yml configuration file. For example, you can prevent the bam_rseqc subworkflow installed from nf-core/modules from being updated by adding the following to the .nf-core.yml file:

update:
  https://github.com/nf-core/modules.git:
    nf-core:
      bam_rseqc: False

If you want this subworkflow to be updated only to a specific version (or downgraded), you could instead specifiy the version:

update:
  https://github.com/nf-core/modules.git:
    nf-core:
      bam_rseqc: "36a77f7c6decf2d1fb9f639ae982bc148d6828aa"

This also works at the repository level. For example, if you want to exclude all modules and subworkflows installed from nf-core/modules from being updated you could add:

update:
  https://github.com/nf-core/modules.git:
    nf-core: False

or if you want all subworkflows in nf-core/modules at a specific version:

update:
  https://github.com/nf-core/modules.git:
    nf-core: "e937c7950af70930d1f34bb961403d9d2aa81c7"

Note that the subworkflow versions specified in the .nf-core.yml file has higher precedence than versions specified with the command line flags, thus aiding you in writing reproducible pipelines.