fix old nf-core sync command and use the info from .nf-core.yml to sy…

…nc a pipeline

nf_core/__main__.py

@@ -1815,6 +1815,7 @@ def command_create_logo(logo_text, directory, name, theme, width, format, force)
 
 # nf-core sync (deprecated)
 @nf_core_cli.command("sync", hidden=True, deprecated=True)
+@click.pass_context
 @click.option(
  "-d",
  "--dir",
@@ -1845,14 +1846,14 @@ def command_create_logo(logo_text, directory, name, theme, width, format, force)
 @click.option("-g", "--github-repository", type=str, help="GitHub PR: target repository.")
 @click.option("-u", "--username", type=str, help="GitHub PR: auth username.")
 @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template")
-def command_sync(directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr):
+def command_sync(ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr):
  """
  Use `nf-core pipelines sync` instead.
  """
  log.warning(
  "The `[magenta]nf-core sync[/]` command is deprecated. Use `[magenta]nf-core pipelines sync[/]` instead."
  )
- pipelines_sync(directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr)
+ pipelines_sync(ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr)
 
 
 # nf-core bump-version (deprecated)

nf_core/utils.py

@@ -1136,6 +1136,45 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path]
  error_message += f"\n{error['loc'][0]}: {error['msg']}"
  raise AssertionError(error_message)
 
+ # Retrieve information if template from config file is empty
+ wf_config = fetch_wf_config(Path(directory))
+ config_template_keys = tools_config["template"].keys() if "template" in tools_config else []
+ if nf_core_yaml_config.template is None:
+ # The .nf-core.yml file did not contain template information
+ nf_core_yaml_config.template = NFCoreTemplateConfig(
+ org="nf-core",
+ name=wf_config["manifest.name"].strip('"').strip("'").split("/")[-1],
+ description=wf_config["manifest.description"].strip('"').strip("'"),
+ author=wf_config["manifest.author"].strip('"').strip("'"),
+ version=wf_config["manifest.version"].strip('"').strip("'"),
+ outdir=str(directory),
+ )
+ elif "prefix" in config_template_keys or "skip" in config_template_keys:
+ # The .nf-core.yml file contained the old prefix or skip keys
+ nf_core_yaml_config.template = NFCoreTemplateConfig(
+ org=tools_config["template"]["prefix"]
+ if "prefix" in config_template_keys
+ else tools_config["template"]["org"] or "nf-core",
+ name=tools_config["template"]["name"]
+ if "name" in config_template_keys
+ else wf_config["manifest.name"].strip('"').strip("'").split("/")[-1],
+ description=tools_config["template"]["description"]
+ if "description" in config_template_keys
+ else wf_config["manifest.description"].strip('"').strip("'"),
+ author=tools_config["template"]["author"]
+ if "author" in config_template_keys
+ else wf_config["manifest.author"].strip('"').strip("'"),
+ version=tools_config["template"]["version"]
+ if "version" in config_template_keys
+ else wf_config["manifest.version"].strip('"').strip("'"),
+ outdir=tools_config["template"]["outdir"] if "outdir" in config_template_keys else str(directory),
+ skip_features=tools_config["template"]["skip"]
+ if "skip" in config_template_keys
+ else tools_config["template"]["skip_features"]
+ if "skip_features" in config_template_keys
+ else None,
+ )
+
  log.debug("Using config file: %s", config_fn)
  return config_fn, nf_core_yaml_config