Merge pull request #3914 from nf-core/dev

Author: mashehu

.github/workflows/sync.yml

@@ -117,8 +117,8 @@ jobs:
             --from-branch dev \
             --pull-request \
             --username nf-core-bot \
-            --github-repository nf-core/${{ matrix.pipeline }}
-            --blogpost ${{inputs.blogpost}}
+            --github-repository nf-core/${{ matrix.pipeline }} \
+            --blog-post ${{inputs.blog_post}}
 
       - name: Upload sync log file artifact
         if: ${{ always() }}

CHANGELOG.md

@@ -1,5 +1,12 @@
 # nf-core/tools: Changelog
 
+## [v3.5.1 - Terne Topi](https://github.com/nf-core/tools/releases/tag/3.5.1) - [2025-11-19]
+
+### General
+
+- Fix `blog_post` parameter for `nf-core pipelines sync` command ([#3911](https://github.com/nf-core/tools/pull/3911))
+- Fix markdown in sync PR message ([#3913](https://github.com/nf-core/tools/pull/3913))
+
 ## [v3.5.0 - Terne Topi](https://github.com/nf-core/tools/releases/tag/3.5.0) - [2025-11-19]
 
 ### General

nf_core/__main__.py

@@ -612,13 +612,16 @@ def rocrate(
 @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")
+@click.option("-b", "--blog-post", type=str, help="Link to the blog post")
 def command_pipelines_sync(
-    ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr
+    ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr, blog_post
 ):
     """
     Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template.
     """
-    pipelines_sync(ctx, 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, blog_post
+    )
 
 
 # nf-core pipelines bump-version

nf_core/commands_pipelines.py

@@ -306,7 +306,9 @@ def pipelines_rocrate(
 
 
 # nf-core pipelines sync
-def pipelines_sync(ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr):
+def pipelines_sync(
+    ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr, blog_post
+):
     """
     Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template.
 
@@ -327,7 +329,7 @@ def pipelines_sync(ctx, directory, from_branch, pull_request, github_repository,
         is_pipeline_directory(directory)
         # Sync the given pipeline dir
         sync_obj = PipelineSync(
-            directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr
+            directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr, blog_post
         )
         sync_obj.sync()
     except (SyncExceptionError, PullRequestExceptionError) as e:

nf_core/pipelines/sync.py

@@ -409,20 +409,21 @@ def make_pull_request(self):
         log.info("Submitting a pull request via the GitHub API")
 
         pr_title = f"Important! Template update for nf-core/tools v{nf_core.__version__}"
+        blog_post_sentence = (
+            f"For more details, check out the blog post: {self.blog_post}" if self.blog_post != "" else ""
+        )
         pr_body_text = (
             "Version `{tag}` of [nf-core/tools](https://github.com/nf-core/tools) has just been released with updates to the nf-core template. "
-            f"For more details, check out the blog post: {self.blog_post}\n\n"
-            if self.blog_post != ""
-            else ""
+            f"{blog_post_sentence}\n\n"
             "Please make sure to merge this pull-request as soon as possible, "
             f"resolving any merge conflicts in the `{self.merge_branch}` branch (or your own fork, if you prefer). "
             "Once complete, make a new minor release of your pipeline.\n\n"
             "For instructions on how to merge this PR, please see "
             "[https://nf-co.re/docs/contributing/sync/](https://nf-co.re/docs/contributing/sync/#merging-automated-prs).\n\n"
             "For more information about this release of [nf-core/tools](https://github.com/nf-core/tools), "
             "please see the `v{tag}` [release page](https://github.com/nf-core/tools/releases/tag/{tag})."
-            "> [!NOTE]\n"
-            "> Since nf-core/tools 3.5.0, older template update PRs will not be automatically closed, but will remain open in your pipeline repository."
+            "\n\n> [!NOTE]\n"
+            "> Since nf-core/tools 3.5.0, older template update PRs will not be automatically closed, but will remain open in your pipeline repository. "
             "Older template PRs will be automatically closed once a newer template PR has been merged."
         ).format(tag=nf_core.__version__)