Merge pull request #3200 from nf-core/dev

Dev -> main

.github/PULL_REQUEST_TEMPLATE.md

@@ -6,7 +6,7 @@ These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a release.
 
-Learn more about contributing: https://github.com/nf-core/tools/tree/master/.github/CONTRIBUTING.md
+Learn more about contributing: https://github.com/nf-core/tools/tree/main/.github/CONTRIBUTING.md
 -->
 
 ## PR checklist

.github/RELEASE_CHECKLIST.md

@@ -6,10 +6,10 @@
 4. Check that modules/subworkflows in template are up to date with the latest releases
 5. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py` and change the gitpod container to `nfcore/gitpod:latest`.
 6. Make sure all CI tests are passing!
-7. Create a PR from `dev` to `master`
-8. Make sure all CI tests are passing again (additional tests are run on PRs to `master`)
+7. Create a PR from `dev` to `main`
+8. Make sure all CI tests are passing again (additional tests are run on PRs to `main`)
 9. Request review (2 approvals required)
-10. Merge the PR into `master`
+10. Merge the PR into `main`
 11. Wait for CI tests on the commit to passed
 12. (Optional but a good idea) Run a manual sync on `nf-core/testpipeline` and check that CI is passing on the resulting PR.
 13. Create a new release copying the `CHANGELOG` for that release into the description section.

.github/workflows/branch.yml

@@ -1,15 +1,15 @@
 name: nf-core branch protection
-# This workflow is triggered on PRs to master branch on the repository
-# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+# This workflow is triggered on PRs to main branch on the repository
+# It fails when someone tries to make a PR against the nf-core `main` branch instead of `dev`
 on:
   pull_request_target:
-    branches: [master]
+    branches: [main]
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      # PRs to the nf-core repo main branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == 'nf-core/tools'
         run: |
@@ -21,7 +21,7 @@ jobs:
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
-            ## This PR is against the `master` branch :x:
+            ## This PR is against the `main` branch :x:
 
             * Do not close this PR
             * Click _Edit_ and change the `base` to `dev`
@@ -31,9 +31,9 @@ jobs:
 
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
-            The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `main` branch.
+            The `main` branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to `main` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
             Note that even after this, the test will continue to show as failing until you push a new commit.

.github/workflows/pytest.yml

@@ -49,7 +49,7 @@ jobs:
     steps:
       - name: Check conditions
         id: conditions
-        run: echo "run-tests=${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> "$GITHUB_OUTPUT"
+        run: echo "run-tests=${{ github.ref == 'refs/heads/main' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> "$GITHUB_OUTPUT"
 
     outputs:
       python-version: ${{ matrix.python-version }}

CHANGELOG.md

@@ -10,8 +10,9 @@
 - We replaced nf-validation with nf-schema in the pipeline template
 - CI tests now lint with the nf-core tools version matching the template version of the pipeline, to minimise errors in opened PRs with every new tools release.
 - `nf-core licences` command is deprecated.
-- The structure of nf-core/tools pytests has been updated
-- The structure of the API docs has been updated
+- Changed default branch to `main`.
+- The structure of nf-core/tools pytests has been updated.
+- The structure of the API docs has been updated.
 
 ### Template
 
@@ -85,6 +86,7 @@
 
 ### General
 
+- Change default branch to `main` for the nf-core/tools repository
 - Update output of generation script for API docs to new structure ([#2988](https://github.com/nf-core/tools/pull/2988))
 - Remove `rich-codex.yml` action, images are now generated on the website repo ([#2989](https://github.com/nf-core/tools/pull/2989))
 - Add no clobber and put bash options on their own line ([#2991](https://github.com/nf-core/tools/pull/2991))

README.md

@@ -1,12 +1,12 @@
 <h1>
   <picture>
-    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/nf-core/tools/master/docs/images/nfcore-tools_logo_dark.png">
-    <img alt="nf-core/tools" src="https://raw.githubusercontent.com/nf-core/tools/master/docs/images/nfcore-tools_logo_light.png">
+    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/nf-core/tools/main/docs/images/nfcore-tools_logo_dark.png">
+    <img alt="nf-core/tools" src="https://raw.githubusercontent.com/nf-core/tools/main/docs/images/nfcore-tools_logo_light.png">
   </picture>
 </h1><!-- omit in toc -->
 
-[![Python tests](https://github.com/nf-core/tools/workflows/Python%20tests/badge.svg?branch=master&event=push)](https://github.com/nf-core/tools/actions?query=workflow%3A%22Python+tests%22+branch%3Amaster)
-[![codecov](https://codecov.io/gh/nf-core/tools/branch/master/graph/badge.svg)](https://codecov.io/gh/nf-core/tools)
+[![Python tests](https://github.com/nf-core/tools/workflows/Python%20tests/badge.svg?branch=main&event=push)](https://github.com/nf-core/tools/actions?query=workflow%3A%22Python+tests%22+branch%3Amain)
+[![codecov](https://codecov.io/gh/nf-core/tools/branch/main/graph/badge.svg)](https://codecov.io/gh/nf-core/tools)
 [![code style: prettier](https://img.shields.io/badge/code%20style-prettier-ff69b4.svg)](https://github.com/prettier/prettier)
 [![code style: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v1.json)](https://github.com/charliermarsh/ruff)
 

docs/api/_src/conf.py

@@ -51,8 +51,8 @@
 # source_suffix = ['.rst', '.md']
 source_suffix = ".rst"
 
-# The master toctree document.
-master_doc = "index"
+# The main toctree document.
+main_doc = "index"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -133,15 +133,15 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, "nf-core.tex", "nf-core tools API documentation", "Phil Ewels, Sven Fillinger", "manual"),
+    (main_doc, "nf-core.tex", "nf-core tools API documentation", "Phil Ewels, Sven Fillinger", "manual"),
 ]
 
 
 # -- Options for manual page output ------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, "nf-core", "nf-core tools API documentation", [author], 1)]
+man_pages = [(main_doc, "nf-core", "nf-core tools API documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -151,7 +151,7 @@
 #  dir menu entry, description, category)
 texinfo_documents = [
     (
-        master_doc,
+        main_doc,
         "nf-core",
         "nf-core tools API documentation",
         author,

nf_core/components/create.py

@@ -248,7 +248,7 @@ def _get_module_structure_components(self):
         if self.process_label is None:
             log.info(
                 "Provide an appropriate resource label for the process, taken from the "
-                "[link=https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config#L29]nf-core pipeline template[/link].\n"
+                "[link=https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config#L29]nf-core pipeline template[/link].\n"
                 "For example: {}".format(", ".join(process_label_defaults))
             )
         while self.process_label is None:

nf_core/pipeline-template/.github/CONTRIBUTING.md

@@ -105,7 +105,7 @@ Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json
 
 ### Default processes resource requirements
 
-Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
 The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 

nf_core/pipeline-template/README.md

@@ -128,7 +128,7 @@ An extensive list of references for the tools used by the pipeline can be found
 You can cite the `nf-core` publication as follows:
 
 {% else -%}
-This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).
+This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).
 
 {% endif -%}