nf_core.list

Lists available nf-core pipelines and versions.

classnf_core.list.LocalWorkflow(name)

Bases: object

Class to handle local workflows pulled by nextflow

get_local_nf_workflow_details()

Get full details about a local cached workflow

classnf_core.list.RemoteWorkflow(data)

Bases: object

A information container for a remote workflow.

• Parameters: data (dict) – workflow information as they are retrieved from the GitHub repository REST API request (https://developer.github.com/v3/repos/#get).

classnf_core.list.Workflows(filter_by=None, sort_by='release', show_archived=False)

Bases: object

Workflow container class.

Is used to collect local and remote nf-core pipelines. Pipelines can be sorted, filtered and compared.

• Parameters:
  • filter_by (list) – A list of strings that can be used for filtering.
  • sort_by (str) – workflows can be sorted by keywords. Keyword must be one of release (default), name, stars.

compare_remote_local()

Matches local to remote workflows.

If a matching remote workflow is found, the local workflow’s Git commit hash is compared with the latest one from remote.

A boolean flag in RemoteWorkflow.local_is_latest is set to True, if the local workflow is the latest.

filtered_workflows()

Filters remote workflows for keywords.

• Returns: Filtered remote workflows.
• Return type: list

get_local_nf_workflows()

Retrieves local Nextflow workflows.

Local workflows are stored in self.local_workflows list.

get_remote_workflows()

Retrieves remote workflows from nf-co.re.

Remote workflows are stored in self.remote_workflows list.

print_json()

Dump JSON of all parsed information

print_summary()

Prints a summary of all pipelines.

nf_core.list.get_local_wf(workflow: str | Path, revision=None)

Check if this workflow has a local copy and use nextflow to pull it if not

nf_core.list.list_workflows(filter_by=None, sort_by='release', as_json=False, show_archived=False)

Prints out a list of all nf-core workflows.

• Parameters:
  • filter_by (list) – A list of strings that can be used for filtering.
  • sort_by (str) – workflows can be sorted by keywords. Keyword must be one of release (default), name, stars.
  • as_json (boolean) – Set to true, if the lists should be printed in JSON.

nf_core.list.pretty_date(time)

Transforms a datetime object or a int() Epoch timestamp into a pretty string like ‘an hour ago’, ‘Yesterday’, ‘3 months ago’, ‘just now’, etc

Based on https://stackoverflow.com/a/1551394/713980 Adapted by sven1103