Save template info

.github/workflows/create-test-lint-wf-template.yml

@@ -97,7 +97,7 @@ jobs:
 
       # Try syncing it before we change anything
       - name: nf-core sync
-        run: nf-core --log-file log.txt sync --dir my-prefix-testpipeline/ --template-yaml ${{ matrix.TEMPLATE }}
+        run: nf-core --log-file log.txt sync --dir my-prefix-testpipeline/
 
       # Run code style linting
       - name: Run Prettier --check

CHANGELOG.md

@@ -8,6 +8,7 @@
 - Remove default false from nextflow_schema.json ([#2376](https://github.com/nf-core/tools/pull/2376))
 - Add module MULTIQC to modules.config ([#2377](https://github.com/nf-core/tools/pull/2377))
 - Update the Code of Conduct ([#2381](https://github.com/nf-core/tools/pull/2381))
+- Save template information to `.nf-core.yml` and deprecate argument `--template-yaml` for `nf-core sync` ([#2388](https://github.com/nf-core/tools/pull/2388) and [#2389](https://github.com/nf-core/tools/pull/2389))
 
 ### Download
 

nf_core/create.py

@@ -96,10 +96,16 @@ def create_param_dict(self, name, description, author, version, template_yaml_pa
         Args:
             template_yaml_path (str): Path to YAML file containing template parameters.
         """
+        # Try reading config file
+        _, config_yml = nf_core.utils.load_tools_config()
+
+        # Obtain template customization info from template yaml file or `.nf-core.yml` config file
         try:
             if template_yaml_path is not None:
                 with open(template_yaml_path, "r") as f:
                     template_yaml = yaml.safe_load(f)
+            elif "template" in config_yml:
+                template_yaml = config_yml["template"]
             else:
                 template_yaml = {}
         except FileNotFoundError:
@@ -169,7 +175,6 @@ def create_param_dict(self, name, description, author, version, template_yaml_pa
         param_dict["logo_dark"] = f"{param_dict['name_noslash']}_logo_dark.png"
         param_dict["version"] = version
 
-        _, config_yml = nf_core.utils.load_tools_config()
         if (
             "lint" in config_yml
             and "nextflow_config" in config_yml["lint"]

nf_core/sync.py

@@ -8,9 +8,11 @@
 import shutil
 
 import git
+import questionary
 import requests
 import requests_cache
 import rich
+import yaml
 from git import GitCommandError, InvalidGitRepositoryError
 
 import nf_core
@@ -42,6 +44,7 @@ class PipelineSync:
         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
+        template_yaml_path (str): Path to template.yml file for pipeline creation settings. DEPRECATED
 
     Attributes:
         pipeline_dir (str): Path to target pipeline directory
@@ -52,7 +55,6 @@ class PipelineSync:
         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__(
@@ -80,11 +82,28 @@ 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()
+        self.config_yml_path, self.config_yml = nf_core.utils.load_tools_config()
+
+        # Throw deprecation warning if template_yaml_path is set
+        if template_yaml_path is not None:
+            log.warning(
+                f"The `template_yaml_path` argument is deprecated. Saving pipeline creation settings in .nf-core.yml instead. Please remove {template_yaml_path} file."
+            )
+            if "template" in self.config_yml:
+                overwrite_template = questionary.confirm(
+                    f"A template section already exists in '{self.config_yml_path}'. Do you want to overwrite?",
+                    style=nf_core.utils.nfcore_question_style,
+                    default=False,
+                ).unsafe_ask()
+            if overwrite_template or "template" not in self.config_yml:
+                with open(template_yaml_path, "r") as f:
+                    self.config_yml["template"] = yaml.safe_load(f)
+                with open(self.config_yml_path, "w") as fh:
+                    yaml.safe_dump(self.config_yml, fh)
+                log.info(f"Saved pipeline creation settings to '{self.config_yml_path}'")
+                raise SystemExit(
+                    f"Please commit your changes and delete {template_yaml_path} file. Then run the sync command again."
+                )
 
         # Set up the API auth if supplied on the command line
         self.gh_api = nf_core.utils.gh_api
@@ -213,7 +232,7 @@ 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" or the_file == self.template_yaml_path:
+            if the_file == ".git":
                 continue
             file_path = os.path.join(self.pipeline_dir, the_file)
             log.debug(f"Deleting {file_path}")
@@ -234,10 +253,10 @@ def make_template_pipeline(self):
         # Only show error messages from pipeline creation
         logging.getLogger("nf_core.create").setLevel(logging.ERROR)
 
-        # 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)
+        # Re-write the template yaml info from .nf-core.yml config
+        if "template" in self.config_yml:
+            with open(self.config_yml_path, "w") as config_path:
+                yaml.safe_dump(self.config_yml, config_path)
 
         try:
             nf_core.create.PipelineCreate(
@@ -248,13 +267,9 @@ def make_template_pipeline(self):
                 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 self.template_yaml_path:
-                # 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}")