Merge branch 'dev' into auto-toot

.github/workflows/create-test-lint-wf-template.yml

@@ -97,7 +97,7 @@ jobs:
 
       # Try syncing it before we change anything
       - name: nf-core sync
-        run: nf-core --log-file log.txt sync --dir my-prefix-testpipeline/ --template-yaml ${{ matrix.TEMPLATE }}
+        run: nf-core --log-file log.txt sync --dir my-prefix-testpipeline/
 
       # Run code style linting
       - name: Run Prettier --check

.github/workflows/pytest.yml

@@ -14,12 +14,19 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
+env:
+  GITHUB_TOKEN: ${{ github.token }}
+
 jobs:
   pytest:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.runner }}
     strategy:
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
+        runner: ["ubuntu-latest"]
+        include:
+          - runner: "ubuntu-20.04"
+            python-version: "3.8"
 
     steps:
       - uses: actions/checkout@v3
@@ -35,6 +42,14 @@ jobs:
           python -m pip install --upgrade pip -r requirements-dev.txt
           pip install -e .
 
+      - name: Downgrade git to the Ubuntu official repository's version
+        if: ${{ matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8' }}
+        run: |
+          sudo apt update
+          sudo apt remove git git-man
+          sudo add-apt-repository --remove ppa:git-core/ppa
+          sudo apt install git
+
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:

.github/workflows/tools-api-docs-dev.yml

@@ -45,6 +45,6 @@ jobs:
           username: ${{ secrets.ftp_username}}
           password: ${{ secrets.ftp_password }}
           local-dir: "./docs/api/_build/html/"
-          server-dir: ${{ secrets.ftp_server_dir }}/dev/
+          server-dir: ${{ secrets.ftp_server_old_site_dir }}/dev/
           protocol: ${{ secrets.ftp_protocol }}
           port: ${{ secrets.ftp_port }}

.github/workflows/tools-api-docs-release.yml

@@ -43,6 +43,6 @@ jobs:
           username: ${{ secrets.ftp_username}}
           password: ${{ secrets.ftp_password }}
           local-dir: "./docs/api/_build/html/"
-          server-dir: ${{ secrets.ftp_server_dir }}/${{ matrix.dir }}/
+          server-dir: ${{ secrets.ftp_server_old_site_dir }}/${{ matrix.dir }}/
           protocol: ${{ secrets.ftp_protocol }}
           port: ${{ secrets.ftp_port }}

CHANGELOG.md

@@ -8,13 +8,19 @@
 - Remove default false from nextflow_schema.json ([#2376](https://github.com/nf-core/tools/pull/2376))
 - Add module MULTIQC to modules.config ([#2377](https://github.com/nf-core/tools/pull/2377))
 - Add GitHub workflow for automated release announcements ([#2382](https://github.com/nf-core/tools/pull/2382))
+- Update the Code of Conduct ([#2381](https://github.com/nf-core/tools/pull/2381))
+- Save template information to `.nf-core.yml` and deprecate argument `--template-yaml` for `nf-core sync` ([#2388](https://github.com/nf-core/tools/pull/2388) and [#2389](https://github.com/nf-core/tools/pull/2389))
+- ([#2397](https://github.com/nf-core/tools/pull/2397)) Remove fixed Ubuntu test and added to standard testing matrix
+- ([#2396](https://github.com/nf-core/tools/pull/2396)) Reduce container finding error to warning since the registries are not consistent.
 
 ### Download
 
 - Improved container image resolution and prioritization of http downloads over Docker URIs ([#2364](https://github.com/nf-core/tools/pull/2364)).
 
 ### Linting
 
+- Add new command `nf-core subworkflows lint` ([#2379](https://github.com/nf-core/tools/pull/2379))
+
 ### Modules
 
 ### Subworkflows
@@ -24,6 +30,8 @@
 - Initialise `docker_image_name` to fix `UnboundLocalError` error ([#2374](https://github.com/nf-core/tools/pull/2374))
 - Fix prompt pipeline revision during launch ([#2375](https://github.com/nf-core/tools/pull/2375))
 - Add a `create-params-file` command to create a YAML parameter file for a pipeline containing parameter documentation and defaults. ([#2362](https://github.com/nf-core/tools/pull/2362))
+- Update the Code of Conduct ([#2381](https://github.com/nf-core/tools/pull/2381))
+- Remove `--no-git` option from `nf-core create` ([#2394](https://github.com/nf-core/tools/pull/2394))
 
 # [v2.9 - Chromium Falcon](https://github.com/nf-core/tools/releases/tag/2.9) + [2023-06-29]