dev -> main for 3.1.0 (#3336)

* set default_branch to master for now

* update changelog

* set git defaultBranch to master in sync action

* update changelog

* use nextflow.config to set defaultBranch

* fix path for nextflow.config grep

* change working dir when setting defaultBranch

* fix Changelog

* Be more verbose in approval check action

* fix if clause

* update changelog

* add verbose mode to sync action

* update changelog

* Apply suggestions from code review

* add input debug for workflow_dispatch sync action

* go back to original directory after configuring git defaultBranch

* add more debugging on sync GHA

* echo message to sync GHA

* try exiting pipeline directory before saving defaultBranch

* cleanup debugging echo

* use same ref in checkout as triggered the workflow

* don't set up loggin level to error

* Revert "don't set up loggin level to error [no changelog]"

* Update nf_core/pipeline-template/.github/workflows/awsfulltest.yml

---------

Co-authored-by: Júlia Mir Pedrol <[email protected]>

Author: mashehu

.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:
@@ -62,6 +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 }}
@@ -87,14 +93,29 @@ jobs:
         with:
           version: "latest-everything"
 
+      - name: Set Git default branch from nextflow.config and set git default branch to that or "master"
+
+        run: |
+          pushd nf-core/${{ matrix.pipeline }}
+          defaultBranch=$(grep -B5 -A5 "nextflowVersion" nextflow.config | grep "defaultBranch" | cut -d"=" -f2)
+          if [ -z "$defaultBranch" ]; then
+            defaultBranch="master"
+          fi
+          popd
+          echo "Default branch: $defaultBranch"
+          echo "defaultBranch=$defaultBranch" >> GITHUB_OUTPUT
+          git config --global init.defaultBranch $defaultBranch
+
       - name: Run synchronisation
         if: github.repository == 'nf-core/tools'
         env:
           GITHUB_AUTH_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
         run: |
           git config --global user.email "[email protected]"
           git config --global user.name "nf-core-bot"
-          nf-core --log-file sync_log_${{ 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 \

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
 
@@ -65,6 +66,9 @@
 - 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))
+- Add verbose mode to sync action ([#3339](https://github.com/nf-core/tools/pull/3339))
 
 ### Version updates
 

nf_core/pipeline-template/.github/workflows/awsfulltest.yml

@@ -19,19 +19,30 @@ 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/[email protected]
+      - name: Get PR reviews
+        uses: octokit/[email protected]
         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:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - id: test_variables
+
+      - name: Check for approvals
+        if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
+        run: |
+          echo "No review approvals found. At least 2 approvals are required to run this action automatically."
+          exit 1
+
+      - name: Check for enough approvals (>=2)
+        id: test_variables
         if: github.event_name != 'workflow_dispatch'
         run: |
           JSON_RESPONSE='${{ 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

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 {

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):
@@ -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("*"))
@@ -431,8 +430,9 @@ 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
+            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"]: