From fa4e07424bf60a42559f4fa756495d7f326eea3c Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 10 Dec 2024 17:17:02 +0100
Subject: [PATCH 1/4] add verbose mode to sync action

---
 .github/workflows/sync.yml         | 6 +++++-
 nf_core/pipelines/create/create.py | 2 +-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index c315fdb14..0e28ece8a 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -88,6 +88,7 @@ jobs:
           version: "latest-everything"
 
       - name: Set Git default branch from nextflow.config and set git default branch to that or "master"
+
         run: |
           cd nf-core/${{ matrix.pipeline }}
           defaultBranch=$(grep -B5 -A5 "nextflowVersion" nextflow.config | grep "defaultBranch" | cut -d"=" -f2)
@@ -95,6 +96,7 @@ jobs:
             defaultBranch="master"
           fi
           echo "Default branch: $defaultBranch"
+          echo "defaultBranch=$defaultBranch" >> GITHUB_OUTPUT
           git config --global init.defaultBranch $defaultBranch
 
       - name: Run synchronisation
@@ -104,7 +106,9 @@ jobs:
         run: |
           git config --global user.email "core@nf-co.re"
           git config --global user.name "nf-core-bot"
-          nf-core --log-file sync_log_${{ matrix.pipeline }}.txt pipelines sync -d nf-core/${{ matrix.pipeline }} \
+          nf-core --log-file sync_log_${{ matrix.pipeline }}.txt
+            ${{ github.event.inputs.debug == 'true' && '--verbose' || '' }}
+            pipelines sync -d nf-core/${{ matrix.pipeline }} \
             --from-branch dev \
             --pull-request \
             --username nf-core-bot \
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index ae5bea57d..0e2c683e6 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -298,7 +298,6 @@ def render_template(self) -> None:
         template_dir = Path(nf_core.__file__).parent / "pipeline-template"
         object_attrs = self.jinja_params
         object_attrs["nf_core_version"] = nf_core.__version__
-
         # Can't use glob.glob() as need recursive hidden dotfiles - https://stackoverflow.com/a/58126417/713980
         template_files = list(Path(template_dir).glob("**/*"))
         template_files += list(Path(template_dir).glob("*"))
@@ -433,6 +432,7 @@ def get_default_branch(self) -> None:
             self.default_branch = (
                 str(git.config.GitConfigParser().get_value("init", "defaultBranch")) or "master"
             )  # default to master
+            log.debug(f"Default branch name: {self.default_branch}")
         except configparser.Error:
             log.debug("Could not read init.defaultBranch")
         if self.default_branch in ["dev", "TEMPLATE"]:

From 5c8937e38b406f5748ebf3ed936de9b1ed0ddaa6 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 10 Dec 2024 17:19:32 +0100
Subject: [PATCH 2/4] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3e1140b65..c23bd9644 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -67,6 +67,7 @@
 - rocrate: Update crate with version bump and handle new contributor field ([#3334](https://github.com/nf-core/tools/pull/3334))
 - set default_branch to master for now ([#3335](https://github.com/nf-core/tools/issues/3335))
 - Set git defaultBranch to master in sync action ([#3337](https://github.com/nf-core/tools/pull/3337))
+- Add verbose mode to sync action ([#3339](https://github.com/nf-core/tools/pull/3339))
 
 ### Version updates
 

From bb3a25294af0326cbbc81857f623bca50a12acc8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Wed, 11 Dec 2024 10:42:54 +0100
Subject: [PATCH 3/4] Apply suggestions from code review

---
 .github/workflows/sync.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 0e28ece8a..15ac0cb00 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -106,8 +106,8 @@ jobs:
         run: |
           git config --global user.email "core@nf-co.re"
           git config --global user.name "nf-core-bot"
-          nf-core --log-file sync_log_${{ matrix.pipeline }}.txt
-            ${{ github.event.inputs.debug == 'true' && '--verbose' || '' }}
+          nf-core --log-file sync_log_${{ matrix.pipeline }}.txt \
+            ${{ github.event.inputs.debug == 'true' && '--verbose' || '' }} \
             pipelines sync -d nf-core/${{ matrix.pipeline }} \
             --from-branch dev \
             --pull-request \

From 379bad0e97a6a1ec407cd9a0705cf5be06557873 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Wed, 11 Dec 2024 10:03:37 +0000
Subject: [PATCH 4/4] add input debug for workflow_dispatch sync action

---
 .github/workflows/sync.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 15ac0cb00..9a1158c3e 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -23,6 +23,10 @@ on:
         description: "Pipeline to sync"
         type: string
         default: "all"
+      debug:
+        description: "Enable debug/verbose mode (true or false)"
+        type: boolean
+        default: false
 
 # Cancel if a newer run is started
 concurrency: