From c0049b08c18c9c442cd6d370376e855e1f5c0fda Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@nonacus.com>
Date: Wed, 5 Oct 2022 12:03:49 +0000
Subject: [PATCH] NF-Core Sync includes template.yaml as option

Fixes #1879
---
 nf_core/__main__.py | 5 +++--
 nf_core/create.py   | 1 +
 nf_core/sync.py     | 5 +++++
 3 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 9df0b2ff97..461a901ec9 100755
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -1054,7 +1054,8 @@ 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.
 
@@ -1071,7 +1072,7 @@ 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:
diff --git a/nf_core/create.py b/nf_core/create.py
index 1cd4fecba0..8b028d90af 100644
--- a/nf_core/create.py
+++ b/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__(
diff --git a/nf_core/sync.py b/nf_core/sync.py
index a663f1c7a7..365d6d1371 100644
--- a/nf_core/sync.py
+++ b/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 +79,8 @@ def __init__(
         self.gh_repo = gh_repo
         self.pr_url = ""
 
+        self.template_yaml_path = template_yaml_path
+
         # Set up the API auth if supplied on the command line
         self.gh_api = nf_core.utils.gh_api
         self.gh_api.lazy_init()
@@ -233,6 +237,7 @@ 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()