nf_core.sync

Synchronise a pipeline TEMPLATE branch with the template.

classnf_core.sync.PipelineSync(pipeline_dir, from_branch=None, make_pr=False, gh_repo=None, gh_username=None, template_yaml_path=None)

Bases: object

Object to hold syncing information and results.

  • Parameters:
    • pipeline_dir (str) – The path to the Nextflow pipeline root directory
    • from_branch (str) – The branch to use to fetch config vars. If not set, will use current active branch
    • make_pr (bool) – Set this to True to create a GitHub pull-request with the changes
    • gh_username (str) – GitHub username
    • gh_repo (str) – GitHub repository name

pipeline_dir

Path to target pipeline directory

  • Type: str

from_branch

Repo branch to use when collecting workflow variables. Default: active branch.

  • Type: str

original_branch

Repo branch that was checked out before we started.

  • Type: str

made_changes

Whether making the new template pipeline introduced any changes

  • Type: bool

make_pr

Whether to try to automatically make a PR on GitHub.com

  • Type: bool

required_config_vars

List of nextflow variables required to make template pipeline

  • Type: list

gh_username

GitHub username

  • Type: str

gh_repo

GitHub repository name

  • Type: str

template_yaml

Path to template.yml file for pipeline creation settings.

  • Type: str

checkout_template_branch()

Try to check out the origin/TEMPLATE in a new TEMPLATE branch. If this fails, try to check out an existing local TEMPLATE branch.

close_open_pr(pr)

Given a PR API response, add a comment and close.

close_open_template_merge_prs()

Get all template merging branches (starting with ‘nf-core-template-merge-‘) and check for any open PRs from these branches to the self.from_branch If open PRs are found, add a comment and close them

commit_template_changes()

If we have any changes with the new template files, make a git commit

create_merge_base_branch()

Create a new branch from the updated TEMPLATE branch This branch will then be used to create the PR

delete_template_branch_files()

Delete all files in the TEMPLATE branch

get_wf_config()

Check out the target branch if requested and fetch the nextflow config. Check that we have the required config variables.

inspect_sync_dir()

Takes a look at the target directory for syncing. Checks that it’s a git repo and makes sure that there are no uncommitted changes.

make_pull_request()

Create a pull request to a base branch (default: dev), from a head branch (default: TEMPLATE)

Returns: An instance of class requests.Response

make_template_pipeline()

Delete all files and make a fresh template using the workflow variables

push_merge_branch()

Push the newly created merge branch to the remote repository

push_template_branch()

If we made any changes, push the TEMPLATE branch to the default remote and try to make a PR. If we don’t have the auth token, try to figure out a URL for the PR and print this to the console.

reset_target_dir()

Reset the target pipeline directory. Check out the original branch.

sync()

Find workflow attributes, create a new template pipeline on TEMPLATE

exceptionnf_core.sync.PullRequestException

Bases: Exception

Exception raised when there was an error creating a Pull-Request on GitHub.com

exceptionnf_core.sync.SyncException

Bases: Exception

Exception raised when there was an error with TEMPLATE branch synchronisation
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