Downloads a nf-core pipeline to the local file system., release=None, singularity=False, outdir=None)

Downloads a nf-core workflow from Github to the local file system.

Can also download its Singularity container image if required.

  • Parameters:
    • pipeline (str) – A nf-core pipeline name.
    • release (str) – The workflow release version to download, like 1.0. Defaults to None.
    • singularity (bool) – Flag, if the Singularity container should be downloaded as well. Defaults to False.
    • outdir (str) – Path to the local download directory. Defaults to None.


Downloads workflow files from Github to the self.outdir.


Starts a nf-core workflow download.


Fetches details of a nf-core workflow to download.

  • Parameters: wfs (nf_core.list.Workflows) – A nf_core.list.Workflows object
  • Raises: LockupError**,** if the pipeline can not be found.


Find container image names for workflow


Uses a local installation of singularity to pull an image from Docker Hub.

  • Parameters: container (str) – A pipeline’s container name. Usually it is of similar format to nfcore/name
  • Raises: Various exceptions possible from subprocess execution of Singularity.

validate_md5(fname, expected)

Calculates the md5sum for a file on the disk and validate with expected.

  • Parameters:
    • fname (str) – Path to a local file.
    • expected (str) – The expected md5sum.
  • Raises: IOError**,** if the md5sum does not match the remote sum.