nf_core.download

Downloads a nf-core pipeline to the local file system.

class nf_core.download.DownloadWorkflow(pipeline, 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.
download_wf_files()

Downloads workflow files from Github to the self.outdir.

download_workflow()

Starts a nf-core workflow download.

fetch_workflow_details(wfs)

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_images()

Find container image names for workflow

pull_singularity_image(container)

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:dev.
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.