nf_core.create

Creates a nf-core pipeline matching the current organization’s specification based on a template.

classnf_core.create.PipelineCreate(name, description, author, version='1.0dev', no_git=False, force=False, outdir=None, template_yaml_path=None, plain=False, default_branch=None)

Bases: object

Creates a nf-core pipeline a la carte from the nf-core best-practice template.

• Parameters:
  • name (str) – Name for the pipeline.
  • description (str) – Description for the pipeline.
  • author (str) – Authors name of the pipeline.
  • version (str) – Version flag. Semantic versioning only. Defaults to 1.0dev.
  • no_git (bool) – Prevents the creation of a local Git repository for the pipeline. Defaults to False.
  • force (bool) – Overwrites a given workflow directory with the same name. Defaults to False. May the force be with you.
  • outdir (str) – Path to the local output directory.
  • template_yaml_path (str) – Path to template.yml file for pipeline creation settings.
  • plain (bool) – If true the Git repository will be initialized plain.
  • default_branch (str) – Specifies the –initial-branch name.

create_param_dict(name, description, author, version, template_yaml_path, plain, pipeline_dir)

Creates a dictionary of parameters for the new pipeline.

• Parameters:
  • name (str) – Name for the pipeline.
  • description (str) – Description for the pipeline.
  • author (str) – Authors name of the pipeline.
  • version (str) – Version flag.
  • template_yaml_path (str) – Path to YAML file containing template parameters.
  • plain (bool) – If true the pipeline template will be initialized plain, without customisation.
  • pipeline_dir (str) – Path to the pipeline directory.

customize_template(template_areas)

Customizes the template parameters.

• Parameters: template_areas (list) – List of available template areas to skip.

fix_linting()

Updates the .nf-core.yml with linting configurations for a customized pipeline.

get_param(param_name, passed_value, template_yaml, template_yaml_path)

git_init_pipeline()

Initialises the new pipeline as a Git repository and submits first commit.

• Raises: UserWarning – if Git default branch is set to ‘dev’ or ‘TEMPLATE’.

init_pipeline()

Creates the nf-core pipeline.

make_pipeline_logo()

Fetch a logo for the new pipeline from the nf-core website

prompt_wf_author()

prompt_wf_description()

prompt_wf_name()

remove_nf_core_in_bug_report_template()

Remove the field mentioning nf-core documentation in the github bug report template

render_template()

Runs Jinja to create a new nf-core pipeline.

update_nextflow_schema()

Removes unused parameters from the nextflow schema.