From b75ba51dba493d8171e1bdb10d13b952a82f405b Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 1 Oct 2024 16:51:32 +0200
Subject: [PATCH] fix old nf-core sync command and use the info from
 .nf-core.yml to sync a pipeline

---
 nf_core/__main__.py |  5 +++--
 nf_core/utils.py    | 39 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 42 insertions(+), 2 deletions(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index e0c1b85e9..08589fc24 100644
--- a/nf_core/__main__.py
+++ b/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)
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 663efb6b4..7795d0d27 100644
--- a/nf_core/utils.py
+++ b/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