nf_core.download

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

classnf_core.download.DownloadWorkflow(pipeline, release=None, singularity=False, outdir=None, compress_type='tar.gz')

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.

compress_download()

Take the downloaded files and make a compressed .tar.gz archive.

download_configs()

Downloads the centralised config profiles from nf-core/configs to self.outdir.

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
  .
• Raises: Various exceptions possible from subprocess execution of Singularity. –

validate_md5(fname, expected=None)

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. –

wf_use_local_configs()

Edit the downloaded nextflow.config file to use the local config files