From e9cde5910a6ebd3e8bccef91a84ee9a47a56381a Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 10 Dec 2024 12:17:54 +0100
Subject: [PATCH 01/24] set default_branch to master for now

---
 nf_core/pipeline-template/nextflow.config | 2 +-
 nf_core/pipelines/create/create.py        | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 000d7cd664..36018b1062 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -327,7 +327,7 @@ validation {
     https://doi.org/10.1038/s41587-020-0439-x
 
 * Software dependencies
-    https://github.com/{{ name }}/blob/master/CITATIONS.md
+    https://github.com/{{ name }}/blob/{{ default_branch }}/CITATIONS.md
 """{% endif %}
     }{% if is_nfcore %}
     summary {
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 8855f2dae3..ae5bea57d5 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -57,7 +57,7 @@ def __init__(
         template_config: Optional[Union[CreateConfig, str, Path]] = None,
         organisation: str = "nf-core",
         from_config_file: bool = False,
-        default_branch: str = "main",
+        default_branch: str = "master",
         is_interactive: bool = False,
     ) -> None:
         if isinstance(template_config, CreateConfig):
@@ -431,8 +431,8 @@ def get_default_branch(self) -> None:
         """Gets the default branch name from the Git configuration."""
         try:
             self.default_branch = (
-                str(git.config.GitConfigParser().get_value("init", "defaultBranch")) or "main"
-            )  # default to main
+                str(git.config.GitConfigParser().get_value("init", "defaultBranch")) or "master"
+            )  # default to master
         except configparser.Error:
             log.debug("Could not read init.defaultBranch")
         if self.default_branch in ["dev", "TEMPLATE"]:

From 7110fff5287cdeb2e5e769d7cf18bd725436f0ad Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 10 Dec 2024 12:20:01 +0100
Subject: [PATCH 02/24] update changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9015ac6daa..4eef49da4d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -81,6 +81,7 @@
 - Parallelize pipeline GHA tests over docker/conda/singularity ([#3214](https://github.com/nf-core/tools/pull/3214))
 - Fix `template_version_comment.yml` github action ([#3212](https://github.com/nf-core/tools/pull/3212))
 - Fix pre-commit linting on pipeline template ([#3218](https://github.com/nf-core/tools/pull/3218))
+- set default_branch to master for now ([#3335](https://github.com/nf-core/tools/issues/3335))
 
 ### Linting
 

From de00162797ddd833a592b918e6405d7f87d26f15 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 10 Dec 2024 13:20:46 +0100
Subject: [PATCH 03/24] set git defaultBranch to master in 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 625f00d247..c1d14d6348 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -87,6 +87,10 @@ jobs:
         with:
           version: "latest-everything"
 
+      - name: Set git defaultBranch to master
+        run: |
+          git config --global init.defaultBranch master
+
       - name: Run synchronisation
         if: github.repository == 'nf-core/tools'
         env:

From 60ae1afaa7e568806602f579ee63577f5c0e4832 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 10 Dec 2024 13:26:07 +0100
Subject: [PATCH 04/24] update changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4eef49da4d..73760131fc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -65,6 +65,7 @@
 - Don't break gitpod.yml with template string ([#3332](https://github.com/nf-core/tools/pull/3332))
 - rocrate: remove duplicated entries for name and version ([#3333](https://github.com/nf-core/tools/pull/3333))
 - rocrate: Update crate with version bump and handle new contributor field ([#3334](https://github.com/nf-core/tools/pull/3334))
+- Set git defaultBranch to master in sync action ([#3337](https://github.com/nf-core/tools/pull/3337))
 
 ### Version updates
 

From 5ee2d52d5ef6a2ffe6e6970b65fbde7e7f7539c8 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 10 Dec 2024 14:30:14 +0100
Subject: [PATCH 05/24] use nextflow.config to set defaultBranch

---
 .github/workflows/sync.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index c1d14d6348..b0464d2741 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -87,9 +87,13 @@ jobs:
         with:
           version: "latest-everything"
 
-      - name: Set git defaultBranch to master
+      - name: Set Git default branch from nextflow.config and set git default branch to that or "master"
         run: |
-          git config --global init.defaultBranch master
+          defaultBranch=$(grep -B5 -A5 "nextflowVersion" nextflow.config | grep "defaultBranch" | cut -d"=" -f2)
+          if [ -z "$defaultBranch" ]; then
+            defaultBranch="master"
+          fi
+          git config --global init.defaultBranch $defaultBranch
 
       - name: Run synchronisation
         if: github.repository == 'nf-core/tools'

From 666fc9f522f8dc94d314758a36bbd260271df7b1 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 10 Dec 2024 14:44:12 +0100
Subject: [PATCH 06/24] fix path for nextflow.config grep

---
 .github/workflows/sync.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index b0464d2741..2a50663971 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -89,7 +89,7 @@ jobs:
 
       - name: Set Git default branch from nextflow.config and set git default branch to that or "master"
         run: |
-          defaultBranch=$(grep -B5 -A5 "nextflowVersion" nextflow.config | grep "defaultBranch" | cut -d"=" -f2)
+          defaultBranch=$(grep -B5 -A5 "nextflowVersion" nf-core/${{ matrix.pipeline }}/nextflow.config | grep "defaultBranch" | cut -d"=" -f2)
           if [ -z "$defaultBranch" ]; then
             defaultBranch="master"
           fi

From 15b044d1b3a1a29b2406d42b5c791fd40e96ce9b Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 10 Dec 2024 15:15:26 +0100
Subject: [PATCH 07/24] change working dir when setting defaultBranch

---
 .github/workflows/sync.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 2a50663971..c315fdb148 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -89,10 +89,12 @@ jobs:
 
       - name: Set Git default branch from nextflow.config and set git default branch to that or "master"
         run: |
-          defaultBranch=$(grep -B5 -A5 "nextflowVersion" nf-core/${{ matrix.pipeline }}/nextflow.config | grep "defaultBranch" | cut -d"=" -f2)
+          cd nf-core/${{ matrix.pipeline }}
+          defaultBranch=$(grep -B5 -A5 "nextflowVersion" nextflow.config | grep "defaultBranch" | cut -d"=" -f2)
           if [ -z "$defaultBranch" ]; then
             defaultBranch="master"
           fi
+          echo "Default branch: $defaultBranch"
           git config --global init.defaultBranch $defaultBranch
 
       - name: Run synchronisation

From 1a22106771d3c6b468e4d3cfb2046157188564cb Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 10 Dec 2024 15:17:06 +0100
Subject: [PATCH 08/24] fix Changelog

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 73760131fc..3e1140b65a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -65,6 +65,7 @@
 - Don't break gitpod.yml with template string ([#3332](https://github.com/nf-core/tools/pull/3332))
 - rocrate: remove duplicated entries for name and version ([#3333](https://github.com/nf-core/tools/pull/3333))
 - 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))
 
 ### Version updates
@@ -82,7 +83,6 @@
 - Parallelize pipeline GHA tests over docker/conda/singularity ([#3214](https://github.com/nf-core/tools/pull/3214))
 - Fix `template_version_comment.yml` github action ([#3212](https://github.com/nf-core/tools/pull/3212))
 - Fix pre-commit linting on pipeline template ([#3218](https://github.com/nf-core/tools/pull/3218))
-- set default_branch to master for now ([#3335](https://github.com/nf-core/tools/issues/3335))
 
 ### Linting
 

From 0b7fe501992f288c8e5164f46ac8fd63d95ddb99 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 10 Dec 2024 15:40:28 +0100
Subject: [PATCH 09/24] Be more verbose in approval check action

---
 .../.github/workflows/awsfulltest.yml            | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
index 45c2a0e555..2a3663bdad 100644
--- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -19,19 +19,29 @@ jobs:
     if: github.repository == '{{ name }}' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
-      - uses: octokit/request-action@v2.x
+      - name: Get PR reviews
+        uses: octokit/request-action@v2.x
         if: github.event_name != 'workflow_dispatch'
         id: check_approvals
         with:
           route: GET /repos/{%- raw -%}${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - id: test_variables
-        if: github.event_name != 'workflow_dispatch'
+
+      - name: Check for approvals
+        if: steps.check_approvals.outputs == ''
+        run: |
+          echo "No approvals found"
+          exit 1
+
+      - name: Check for enough approvals (>=2)
+        id: test_variables
+        if: github.event_name != 'workflow_dispatch' && steps.check_approvals.outputs != ''
         run: |
           JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'{% endraw %}
           CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
           test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
+
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required

From f7ced6bcd6e07baf89e6ee7f67d7f8f8c532ab0e Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 10 Dec 2024 16:00:03 +0100
Subject: [PATCH 10/24] fix if clause

---
 nf_core/pipeline-template/.github/workflows/awsfulltest.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
index 2a3663bdad..cd39124900 100644
--- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -29,14 +29,14 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Check for approvals
-        if: steps.check_approvals.outputs == ''
+        if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
         run: |
-          echo "No approvals found"
+          echo "No review approvals found. At least 2 approvals are required to run this action automatically."
           exit 1
 
       - name: Check for enough approvals (>=2)
         id: test_variables
-        if: github.event_name != 'workflow_dispatch' && steps.check_approvals.outputs != ''
+        if: github.event_name != 'workflow_dispatch'
         run: |
           JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'{% endraw %}
           CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')

From 174861324f70c243c71484d3216c5edfb8f78013 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 10 Dec 2024 16:01:04 +0100
Subject: [PATCH 11/24] update changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3e1140b65a..7d31390ba9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,6 +23,7 @@
 - Add `manifest.contributors` to `nextflow.config` ([#3311](https://github.com/nf-core/tools/pull/3311))
 - Update template components ([#3328](https://github.com/nf-core/tools/pull/3328))
 - Template: Remove mention of GRCh37 if igenomes is skipped ([#3330](https://github.com/nf-core/tools/pull/3330))
+- Be more verbose in approval check action ([#3338](https://github.com/nf-core/tools/pull/3338))
 
 ### Download
 

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 12/24] 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 c315fdb148..0e28ece8a6 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 ae5bea57d5..0e2c683e6f 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 13/24] update changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3e1140b65a..c23bd96442 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 14/24] 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 0e28ece8a6..15ac0cb000 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 15/24] 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 15ac0cb000..9a1158c3ee 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:

From 6148983c8469149cda6e834998cc01c78102f418 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 11 Dec 2024 11:44:22 +0100
Subject: [PATCH 16/24] go back to original directory after configuring git
 defaultBranch

---
 .github/workflows/sync.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 9a1158c3ee..b453331148 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -94,7 +94,7 @@ jobs:
       - name: Set Git default branch from nextflow.config and set git default branch to that or "master"
 
         run: |
-          cd nf-core/${{ matrix.pipeline }}
+          pushd nf-core/${{ matrix.pipeline }}
           defaultBranch=$(grep -B5 -A5 "nextflowVersion" nextflow.config | grep "defaultBranch" | cut -d"=" -f2)
           if [ -z "$defaultBranch" ]; then
             defaultBranch="master"
@@ -102,6 +102,7 @@ jobs:
           echo "Default branch: $defaultBranch"
           echo "defaultBranch=$defaultBranch" >> GITHUB_OUTPUT
           git config --global init.defaultBranch $defaultBranch
+          popd
 
       - name: Run synchronisation
         if: github.repository == 'nf-core/tools'

From df5b3233a38b6732b9f45946fbe6493b8bc73151 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 11 Dec 2024 14:51:17 +0100
Subject: [PATCH 17/24] add more debugging on sync GHA

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

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index b453331148..ea2c6283de 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -111,6 +111,8 @@ jobs:
         run: |
           git config --global user.email "core@nf-co.re"
           git config --global user.name "nf-core-bot"
+          setBranch=$(git config --global init.defaultBranch)
+          echo "set default branch: $setBranch" >> GITHUB_OUTPUT
           nf-core --log-file sync_log_${{ matrix.pipeline }}.txt \
             ${{ github.event.inputs.debug == 'true' && '--verbose' || '' }} \
             pipelines sync -d nf-core/${{ matrix.pipeline }} \

From 1de1034c0888f515bc26c32559707b24e835890c Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 11 Dec 2024 15:34:37 +0100
Subject: [PATCH 18/24] echo message to sync GHA

---
 .github/workflows/sync.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index ea2c6283de..26c11c827e 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -112,7 +112,7 @@ jobs:
           git config --global user.email "core@nf-co.re"
           git config --global user.name "nf-core-bot"
           setBranch=$(git config --global init.defaultBranch)
-          echo "set default branch: $setBranch" >> GITHUB_OUTPUT
+          echo "set default branch: $setBranch"
           nf-core --log-file sync_log_${{ matrix.pipeline }}.txt \
             ${{ github.event.inputs.debug == 'true' && '--verbose' || '' }} \
             pipelines sync -d nf-core/${{ matrix.pipeline }} \

From 3858e38a5410684bfd58a1f6a27bcc4dc65fa81a Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 11 Dec 2024 16:03:12 +0100
Subject: [PATCH 19/24] try exiting pipeline directory before saving
 defaultBranch

---
 .github/workflows/sync.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 26c11c827e..23e89c26c4 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -99,10 +99,10 @@ jobs:
           if [ -z "$defaultBranch" ]; then
             defaultBranch="master"
           fi
+          popd
           echo "Default branch: $defaultBranch"
           echo "defaultBranch=$defaultBranch" >> GITHUB_OUTPUT
           git config --global init.defaultBranch $defaultBranch
-          popd
 
       - name: Run synchronisation
         if: github.repository == 'nf-core/tools'

From 380be6c2c20cd8306bd73089b3999bea21440e89 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 11 Dec 2024 16:10:05 +0100
Subject: [PATCH 20/24] cleanup debugging echo

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

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 23e89c26c4..4d7c496eda 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -111,8 +111,6 @@ jobs:
         run: |
           git config --global user.email "core@nf-co.re"
           git config --global user.name "nf-core-bot"
-          setBranch=$(git config --global init.defaultBranch)
-          echo "set default branch: $setBranch"
           nf-core --log-file sync_log_${{ matrix.pipeline }}.txt \
             ${{ github.event.inputs.debug == 'true' && '--verbose' || '' }} \
             pipelines sync -d nf-core/${{ matrix.pipeline }} \

From be38c157038786f6e1ae60ce82ffa666674d9d0e Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 11 Dec 2024 20:06:58 +0100
Subject: [PATCH 21/24] use same ref in checkout as triggered the workflow

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

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 4d7c496eda..7061294783 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -66,6 +66,8 @@ jobs:
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out nf-core/tools
+        with:
+          ref: ${{ github.ref_name }}
 
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out nf-core/${{ matrix.pipeline }}

From e92f327cdc75e93253524b4e1c277e9ea8d91149 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 12 Dec 2024 10:00:43 +0100
Subject: [PATCH 22/24] don't set up loggin level to error

---
 nf_core/pipelines/sync.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py
index 781b4f5f00..a75ddef33b 100644
--- a/nf_core/pipelines/sync.py
+++ b/nf_core/pipelines/sync.py
@@ -261,7 +261,7 @@ def make_template_pipeline(self):
         log.info("Making a new template pipeline using pipeline variables")
 
         # Only show error messages from pipeline creation
-        logging.getLogger("nf_core.pipelines.create").setLevel(logging.ERROR)
+        # logging.getLogger("nf_core.pipelines.create").setLevel(logging.ERROR)
         assert self.config_yml_path is not None
         assert self.config_yml is not None
 

From 8f00659ca4c54144eee4415a98dedad1eaf87d67 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?=
 <mashehu@users.noreply.github.com>
Date: Thu, 12 Dec 2024 10:59:54 +0100
Subject: [PATCH 23/24] Revert "don't set up loggin level to error [no
 changelog]"

---
 nf_core/pipelines/sync.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py
index a75ddef33b..781b4f5f00 100644
--- a/nf_core/pipelines/sync.py
+++ b/nf_core/pipelines/sync.py
@@ -261,7 +261,7 @@ def make_template_pipeline(self):
         log.info("Making a new template pipeline using pipeline variables")
 
         # Only show error messages from pipeline creation
-        # logging.getLogger("nf_core.pipelines.create").setLevel(logging.ERROR)
+        logging.getLogger("nf_core.pipelines.create").setLevel(logging.ERROR)
         assert self.config_yml_path is not None
         assert self.config_yml is not None
 

From c2a9dee17bc981f0b20bcea7dc167a620d409bb9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Thu, 12 Dec 2024 11:14:52 +0100
Subject: [PATCH 24/24] Update
 nf_core/pipeline-template/.github/workflows/awsfulltest.yml

---
 nf_core/pipeline-template/.github/workflows/awsfulltest.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
index cd39124900..6805c83a27 100644
--- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -23,6 +23,7 @@ jobs:
         uses: octokit/request-action@v2.x
         if: github.event_name != 'workflow_dispatch'
         id: check_approvals
+        continue-on-error: true
         with:
           route: GET /repos/{%- raw -%}${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
         env: