Merge pull request #1880 from adamrtalbot/1879_sync_template_yaml

NF-Core Sync includes template.yaml as option

CHANGELOG.md

@@ -11,6 +11,7 @@
 ### General
 
 - Fix error in tagging GitPod docker images during releases
+- `nf-core sync` now supports the template YAML file using `-t/--template-yaml`.
 - Fix bug when updating modules from old version in old folder structure
 - Don't remove local copy of modules repo, only update it with fetch ([#1881](https://github.com/nf-core/tools/pull/1881))
 - Add subworkflow commands create-test-yml, create and install ([#1897](https://github.com/nf-core/tools/pull/1897))

nf_core/__main__.py

@@ -1197,7 +1197,8 @@ def bump_version(new_version, dir, nextflow):
 @click.option("-p", "--pull-request", is_flag=True, default=False, help="Make a GitHub pull-request with the changes.")
 @click.option("-g", "--github-repository", type=str, help="GitHub PR: target repository.")
 @click.option("-u", "--username", type=str, help="GitHub PR: auth username.")
-def sync(dir, from_branch, pull_request, github_repository, username):
+@click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template")
+def sync(dir, from_branch, pull_request, github_repository, username, template_yaml):
  """
  Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template.
 
@@ -1214,7 +1215,7 @@ def sync(dir, from_branch, pull_request, github_repository, username):
  nf_core.utils.is_pipeline_directory(dir)
 
  # Sync the given pipeline dir
- sync_obj = nf_core.sync.PipelineSync(dir, from_branch, pull_request, github_repository, username)
+ sync_obj = nf_core.sync.PipelineSync(dir, from_branch, pull_request, github_repository, username, template_yaml)
  try:
  sync_obj.sync()
  except (nf_core.sync.SyncException, nf_core.sync.PullRequestException) as e:

nf_core/create.py

@@ -39,6 +39,7 @@ class PipelineCreate(object):
  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 (str): Path to template.yml file for pipeline creation settings.
  """
 
  def __init__(

nf_core/sync.py

@@ -52,6 +52,7 @@ class PipelineSync(object):
  required_config_vars (list): List of nextflow variables required to make template pipeline
  gh_username (str): GitHub username
  gh_repo (str): GitHub repository name
+ template_yaml (str): Path to template.yml file for pipeline creation settings.
  """
 
  def __init__(
@@ -61,6 +62,7 @@ def __init__(
  make_pr=False,
  gh_repo=None,
  gh_username=None,
+ template_yaml_path=None,
  ):
  """Initialise syncing object"""
 
@@ -77,6 +79,12 @@ def __init__(
  self.gh_repo = gh_repo
  self.pr_url = ""
 
+ self.template_yaml_path = template_yaml_path
+ # Save contents of template.yml for using outside of git.
+ if self.template_yaml_path is not None:
+ with open(self.template_yaml_path, "r") as template_yaml:
+ self.template_yaml_cache = template_yaml.read()
+
  # Set up the API auth if supplied on the command line
  self.gh_api = nf_core.utils.gh_api
  self.gh_api.lazy_init()
@@ -204,7 +212,7 @@ def delete_template_branch_files(self):
  # Delete everything
  log.info("Deleting all files in 'TEMPLATE' branch")
  for the_file in os.listdir(self.pipeline_dir):
- if the_file == ".git":
+ if the_file == ".git" or the_file == self.template_yaml_path:
  continue
  file_path = os.path.join(self.pipeline_dir, the_file)
  log.debug(f"Deleting {file_path}")
@@ -225,16 +233,29 @@ def make_template_pipeline(self):
  # Only show error messages from pipeline creation
  logging.getLogger("nf_core.create").setLevel(logging.ERROR)
 
- nf_core.create.PipelineCreate(
- name=self.wf_config["manifest.name"].strip('"').strip("'"),
- description=self.wf_config["manifest.description"].strip('"').strip("'"),
- version=self.wf_config["manifest.version"].strip('"').strip("'"),
- no_git=True,
- force=True,
- outdir=self.pipeline_dir,
- author=self.wf_config["manifest.author"].strip('"').strip("'"),
- plain=True,
- ).init_pipeline()
+ # Re-write the template yaml from cache which may have been updated
+ if self.template_yaml_path and self.template_yaml_cache:
+ with open(self.template_yaml_path, "w") as template_path:
+ template_path.write(self.template_yaml_cache)
+
+ try:
+ nf_core.create.PipelineCreate(
+ name=self.wf_config["manifest.name"].strip('"').strip("'"),
+ description=self.wf_config["manifest.description"].strip('"').strip("'"),
+ version=self.wf_config["manifest.version"].strip('"').strip("'"),
+ no_git=True,
+ force=True,
+ outdir=self.pipeline_dir,
+ author=self.wf_config["manifest.author"].strip('"').strip("'"),
+ template_yaml_path=self.template_yaml_path,
+ plain=True,
+ ).init_pipeline()
+ except Exception as err:
+ # If sync fails, remove template_yaml_path before raising error.
+ os.remove(self.template_yaml_path)
+ # Reset to where you were to prevent git getting messed up.
+ self.repo.git.reset("--hard")
+ raise SyncException(f"Failed to rebuild pipeline from template with error:\n{err}")
 
  def commit_template_changes(self):
  """If we have any changes with the new template files, make a git commit"""