Merge pull request #3185 from mirpedrol/sync-fixes

Fix nf-core pipelines sync

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/pipelines/create/create.py

@@ -182,7 +182,7 @@ def update_config(self, organisation, version, force, outdir):
             self.config.force = force if force else False
         if self.config.outdir is None:
             self.config.outdir = outdir if outdir else "."
-        if self.config.is_nfcore is None:
+        if self.config.is_nfcore is None or self.config.is_nfcore == "null":
             self.config.is_nfcore = self.config.org == "nf-core"
 
     def obtain_jinja_params_dict(
@@ -363,11 +363,9 @@ def render_template(self) -> None:
             config_fn, config_yml = nf_core.utils.load_tools_config(self.outdir)
             if config_fn is not None and config_yml is not None:
                 with open(str(config_fn), "w") as fh:
-                    self.config.outdir = str(self.config.outdir)
                     config_yml.template = NFCoreTemplateConfig(**self.config.model_dump())
                     yaml.safe_dump(config_yml.model_dump(), fh)
                     log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'")
-                    run_prettier_on_file(self.outdir / config_fn)
 
         # Run prettier on files
         run_prettier_on_file(self.outdir)
@@ -401,8 +399,6 @@ def fix_linting(self):
             with open(self.outdir / config_fn, "w") as fh:
                 yaml.dump(nf_core_yml.model_dump(), fh, default_flow_style=False, sort_keys=False)
 
-            run_prettier_on_file(Path(self.outdir, config_fn))
-
     def make_pipeline_logo(self):
         """Fetch a logo for the new pipeline from the nf-core website"""
         email_logo_path = Path(self.outdir) / "assets"

nf_core/pipelines/download.py

@@ -746,7 +746,7 @@ def find_container_images(self, workflow_directory: str) -> None:
                     self.nf_config is needed, because we need to restart search over raw input
                     if no proper container matches are found.
                     """
-                    config_findings.append((k, v.strip('"').strip("'"), self.nf_config, "Nextflow configs"))
+                    config_findings.append((k, v.strip("'\""), self.nf_config, "Nextflow configs"))
 
         # rectify the container paths found in the config
         # Raw config_findings may yield multiple containers, so better create a shallow copy of the list, since length of input and output may be different ?!?

nf_core/pipelines/schema.py

@@ -71,7 +71,7 @@ def _update_validation_plugin_from_config(self) -> None:
         else:
             conf = nf_core.utils.fetch_wf_config(Path(self.pipeline_dir))
 
-        plugins = str(conf.get("plugins", "")).strip('"').strip("'").strip(" ").split(",")
+        plugins = str(conf.get("plugins", "")).strip("'\"").strip(" ").split(",")
         plugin_found = False
         for plugin_instance in plugins:
             if "nf-schema" in plugin_instance:
@@ -373,7 +373,7 @@ def validate_config_default_parameter(self, param, schema_param, config_default)
         # If we have a default in the schema, check it matches the config
         if "default" in schema_param and (
             (schema_param["type"] == "boolean" and str(config_default).lower() != str(schema_param["default"]).lower())
-            and (str(schema_param["default"]) != str(config_default).strip('"').strip("'"))
+            and (str(schema_param["default"]) != str(config_default).strip("'\""))
         ):
             # Check that we are not deferring the execution of this parameter in the schema default with squiggly brakcets
             if schema_param["type"] != "string" or "{" not in schema_param["default"]:

nf_core/pipelines/sync.py

@@ -273,17 +273,23 @@ def make_template_pipeline(self):
                 yaml.safe_dump(self.config_yml.model_dump(), config_path)
 
         try:
-            nf_core.pipelines.create.create.PipelineCreate(
+            pipeline_create_obj = nf_core.pipelines.create.create.PipelineCreate(
                 outdir=str(self.pipeline_dir),
                 from_config_file=True,
                 no_git=True,
                 force=True,
-            ).init_pipeline()
+            )
+            pipeline_create_obj.init_pipeline()
 
             # set force to false to avoid overwriting files in the future
             if self.config_yml.template is not None:
+                self.config_yml.template = pipeline_create_obj.config
                 # Set force true in config to overwrite existing files
                 self.config_yml.template.force = False
+                # Set outdir as the current directory to avoid local info leaking
+                self.config_yml.template.outdir = "."
+                # Update nf-core version
+                self.config_yml.nf_core_version = nf_core.__version__
                 with open(self.config_yml_path, "w") as config_path:
                     yaml.safe_dump(self.config_yml.model_dump(), config_path)
 

nf_core/utils.py

@@ -1136,6 +1136,35 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path]
             error_message += f"\n{error['loc'][0]}: {error['msg']}"
         raise AssertionError(error_message)
 
+    wf_config = fetch_wf_config(Path(directory))
+    if nf_core_yaml_config["repository_type"] == "pipeline" and wf_config:
+        # Retrieve information if template from config file is empty
+        template = tools_config.get("template")
+        config_template_keys = template.keys() if template is not None 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("'\"").split("/")[-1],
+                description=wf_config["manifest.description"].strip("'\""),
+                author=wf_config["manifest.author"].strip("'\""),
+                version=wf_config["manifest.version"].strip("'\""),
+                outdir=str(directory),
+                is_nfcore=True,
+            )
+        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"].get("prefix", tools_config["template"].get("org", "nf-core")),
+                name=tools_config["template"].get("name", wf_config["manifest.name"].strip("'\"").split("/")[-1]),
+                description=tools_config["template"].get("description", wf_config["manifest.description"].strip("'\"")),
+                author=tools_config["template"].get("author", wf_config["manifest.author"].strip("'\"")),
+                version=tools_config["template"].get("version", wf_config["manifest.version"].strip("'\"")),
+                outdir=tools_config["template"].get("outdir", str(directory)),
+                skip_features=tools_config["template"].get("skip", tools_config["template"].get("skip_features")),
+                is_nfcore=tools_config["template"].get("prefix", tools_config["template"].get("org")) == "nf-core",
+            )
+
     log.debug("Using config file: %s", config_fn)
     return config_fn, nf_core_yaml_config