Merge pull request #2257 from nf-core/dev

Dev -> Master for v2.8

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -38,4 +38,4 @@ body:
         * Executor _(eg. slurm, local, awsbatch)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
         * Version of nf-core/tools _(eg. 1.1, 1.5, 1.8.2)_
-        * Python version _(eg. 3.7, 3.8)_
+        * Python version _(eg. 3.10, 3.11)_

.github/RELEASE_CHECKLIST.md

@@ -3,13 +3,13 @@
 1. Check issue milestones to see outstanding issues to resolve if possible or transfer to the milestones for the next release e.g. [`v1.9`](https://github.com/nf-core/tools/issues?q=is%3Aopen+is%3Aissue+milestone%3A1.9)
 2. Most importantly, pick an undeniably outstanding [name](http://www.codenamegenerator.com/) for the release where _Prefix_ = _Metal_ and _Dictionary_ = _Animal_.
 3. Check the [pipeline health page](https://nf-co.re/pipeline_health) to make sure that all repos look sane (missing `TEMPLATE` branches etc)
-4. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py`.
+4. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py` and change the gitpod container to `nfcore/gitpod:latest`.
 5. Make sure all CI tests are passing!
 6. Create a PR from `dev` to `master`
 7. Make sure all CI tests are passing again (additional tests are run on PRs to `master`)
 8. Request review (2 approvals required)
-9. Merge the PR into `master`
-10. Run `rich-codex` to regenerate docs screengrabs (actions `workflow_dispatch` button)
+9. Run `rich-codex` to regenerate docs screengrabs (actions `workflow_dispatch` button)
+10. Merge the PR into `master`
 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.
@@ -19,4 +19,4 @@
 1. Check the automated template synchronisation has been triggered properly. This should automatically open PRs directly to individual pipeline repos with the appropriate changes to update the pipeline template.
 2. Check that the automatic `PyPi` deployment has worked: [pypi.org/project/nf-core](https://pypi.org/project/nf-core/)
 3. Check `BioConda` has an automated PR to bump the version, and merge. eg. [bioconda/bioconda-recipes #20065](https://github.com/bioconda/bioconda-recipes/pull/20065)
-4. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `setup.py`
+4. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `setup.py` and change the gitpod container to `nfcore/gitpod:dev`.

.github/workflows/branch.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/tools'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name}} == nf-core/tools ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name}} == nf-core/tools ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment

.github/workflows/clean-up.yml

@@ -0,0 +1,24 @@
+name: "Close user-tagged issues and PRs"
+on:
+  schedule:
+    - cron: "0 0 * * 0" # Once a week
+
+jobs:
+  clean-up:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@v7
+        with:
+          stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
+          stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
+          close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
+          days-before-stale: 30
+          days-before-close: 20
+          days-before-pr-close: -1
+          any-of-labels: "awaiting-changes,awaiting-feedback"
+          exempt-issue-labels: "WIP"
+          exempt-pr-labels: "WIP"
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

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

@@ -84,6 +84,10 @@ jobs:
       - name: remove TODO
         run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;
 
+      # Replace zenodo.XXXXXX to pass readme linting
+      - name: replace zenodo.XXXXXX
+        run: find nf-core-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
+
       # Run nf-core linting
       - name: nf-core lint
         run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned
@@ -108,7 +112,7 @@ jobs:
         run: nf-core --log-file log.txt modules install fastqc --dir nf-core-testpipeline/ --force
 
       - name: nf-core modules install gitlab
-        run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git --branch main install fastqc --force --dir nf-core-testpipeline/
+        run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git --branch branch-tester install fastp --dir nf-core-testpipeline/
 
       - name: nf-core modules list local
         run: nf-core --log-file log.txt modules list local --dir nf-core-testpipeline/

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

@@ -29,10 +29,10 @@ jobs:
       - uses: actions/checkout@v3
         name: Check out source-code repository
 
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Install python dependencies
         run: |

.github/workflows/deploy-pypi.yml

@@ -16,10 +16,10 @@ jobs:
       - uses: actions/checkout@v3
         name: Check out source-code repository
 
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Install python dependencies
         run: |

.github/workflows/pytest-frozen-ubuntu-20.04.yml

@@ -33,6 +33,7 @@ jobs:
 
       - name: Downgrade git to the Ubuntu official repository's version
         run: |
+          sudo apt update
           sudo apt remove git git-man
           sudo add-apt-repository --remove ppa:git-core/ppa
           sudo apt install git

.github/workflows/pytest.yml

@@ -19,7 +19,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
       - uses: actions/checkout@v3

.github/workflows/rich-codex.yml

@@ -18,7 +18,7 @@ jobs:
         uses: nf-core/setup-nextflow@v1
 
       - name: Install nf-core/tools
-        run: pip install .
+        run: pip install git+https://github.com/nf-core/tools.git@dev
 
       - name: Generate terminal images with rich-codex
         uses: ewels/rich-codex@v1

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

@@ -22,10 +22,10 @@ jobs:
       - name: Check out source-code repository
         uses: actions/checkout@v3
 
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Install python dependencies
         run: |

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

@@ -21,10 +21,10 @@ jobs:
       - name: Check out source-code repository
         uses: actions/checkout@v3
 
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Install python dependencies
         run: |

.pre-commit-config.yaml

@@ -1,14 +1,13 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 23.1.0
     hooks:
       - id: black
-        language_version: python3.9
   - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v2.6.2"
+    rev: "v2.7.1"
     hooks:
       - id: prettier

.prettierignore

@@ -3,4 +3,5 @@ adaptivecard.json
 slackreport.json
 docs/api/_build
 testing
-
+nf_core/module-template/modules/meta.yml
+nf_core/module-template/tests/test.yml

CHANGELOG.md

@@ -1,5 +1,60 @@
 # nf-core/tools: Changelog
 
+# [v2.8 - Ruthenium Monkey](https://github.com/nf-core/tools/releases/tag/2.8) - [2023-04-27]
+
+### Template
+
+- Explicitly disable `conda` when a container profile ([#2140](https://github.com/nf-core/tools/pull/2140))
+- Turn on automatic clean up of intermediate files in `work/` on successful pipeline completion in full-test config ([#2163](https://github.com/nf-core/tools/pull/2163)) [Contributed by @jfy133]
+- Add documentation to `usage.md` on how to use `params.yml` files, based on nf-core/ampliseq text ([#2173](https://github.com/nf-core/tools/pull/2173/)) [Contributed by @jfy133, @d4straub]
+- Make jobs automatically resubmit for a much wider range of exit codes (now `104` and `130..145`) ([#2170](https://github.com/nf-core/tools/pull/2170))
+- Add a clean-up GHA which closes issues and PRs with specific labels ([#2183](https://github.com/nf-core/tools/pull/2183))
+- Remove problematic sniffer code in samplesheet_check.py that could give false positive 'missing header' errors ([https://github.com/nf-core/tools/pull/2194]) [Contributed by @Midnighter, @jfy133]
+- Consistent syntax for branch checks in PRs ([#2202](https://github.com/nf-core/tools/issues/2202))
+- Fixed minor Jinja2 templating bug that caused the PR template to miss a newline
+- Updated AWS tests to use newly moved `seqeralabs/action-tower-launch` instead of `nf-core/tower-action`
+- Remove `.cff` files from `.editorconfig` [(#2145)[https://github.com/nf-core/tools/pull/2145]]
+- Simplify pipeline README ([#2186](https://github.com/nf-core/tools/issues/2186))
+- Added support for the apptainer container engine via `-profile apptainer`. ([#2244](https://github.com/nf-core/tools/issues/2244)) [Contributed by @jfy133]
+- Added config `docker.registry` to pipeline template for a configurable default container registry when using Docker containers. Defaults to `quay.io` ([#2133](https://github.com/nf-core/tools/pull/2133))
+- Add tower.yml file to the pipeline template ([#2251](https://github.com/nf-core/tools/pull/2251))
+- Add mastodon badge to README ([#2253](https://github.com/nf-core/tools/pull/2253))
+- Removed `quay.io` from all module Docker container references as this is now supplied at pipeline level. ([#2249](https://github.com/nf-core/tools/pull/2249))
+- Remove `CITATION.cff` file from pipeline template, to avoid that pipeline Zenodo entries reference the nf-core publication instead of the pipeline ([#2059](https://github.com/nf-core/tools/pull/2059)).
+
+### Linting
+
+- Update modules lint test to fail if enable_conda is found ([#2213](https://github.com/nf-core/tools/pull/2213))
+- Read module lint configuration from `.nf-core.yml`, not `.nf-core-lint.yml` ([#2221](https://github.com/nf-core/tools/pull/2221))
+- `nf-core schema lint` now defaults to linting `nextflow_schema.json` if no filename is provided ([#2225](https://github.com/nf-core/tools/pull/2225))
+- Warn if `/zenodo.XXXXXX` is present in the Readme ([#2254](https://github.com/nf-core/tools/pull/2254))
+- Lint all labels in a module ([#2227](https://github.com/nf-core/tools/pull/2227))
+
+### Modules
+
+- Add an `--empty-template` option to create a module without TODO statements or examples ([#2175](https://github.com/nf-core/tools/pull/2175) & [#2177](https://github.com/nf-core/tools/pull/2177))
+- Removed the `nf-core modules mulled` command and all its code dependencies ([2199](https://github.com/nf-core/tools/pull/2199)).
+- Take into accout the provided `--git_remote` URL when linting all modules ([2243](https://github.com/nf-core/tools/pull/2243)).
+
+### Subworkflows
+
+- Fixing problem when a module included in a subworkflow had a name change from TOOL to TOOL/SUBTOOL ([#2177](https://github.com/nf-core/tools/pull/2177))
+- Fix `nf-core subworkflows test` not running subworkflow tests ([#2181](https://github.com/nf-core/tools/pull/2181))
+- Add tests for `nf-core subworkflows create-test-yml` ([#2219](https://github.com/nf-core/tools/pull/2219))
+
+### General
+
+- Deprecate Python 3.7 support because it reaches EOL ([#2210](https://github.com/nf-core/tools/pull/2210))
+- `nf-core modules/subworkflows info` now prints the include statement for the module/subworkflow ([#2182](https://github.com/nf-core/tools/pull/2182)).
+- Add a clean-up GHA which closes issues and PRs with specific labels ([#2183](https://github.com/nf-core/tools/pull/2183))
+- update minimum version of rich to 13.3.1 ([#2185](https://github.com/nf-core/tools/pull/2185))
+- Add the Nextflow version to Gitpod container matching the minimal Nextflow version for nf-core (according to `nextflow.config`) ([#2196](https://github.com/nf-core/tools/pull/2196))
+- Use `nfcore/gitpod:dev` container in the dev branch ([#2196](https://github.com/nf-core/tools/pull/2196))
+- Replace requests_mock with responses in test mocks ([#2165](https://github.com/nf-core/tools/pull/2165)).
+- Add warning when installing a module from an `org_path` that exists in multiple remotes in `modules.json` ([#2228](https://github.com/nf-core/tools/pull/2228) [#2239](https://github.com/nf-core/tools/pull/2239)).
+- Add the possibility to translate refgenie asset aliases to the ones used in a pipeline with an alias_translations.yaml file ([#2242](https://github.com/nf-core/tools/pull/2242)).
+- Add initial CHM13 support ([1988](https://github.com/nf-core/tools/issues/1988))
+
 ## [v2.7.2 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.2) - [2022-12-19]
 
 ### Template
@@ -49,7 +104,6 @@ Another big release with lots of new features and bug fixes. Thanks to all contr
 
 - Fix lint warnings for `samplesheet_check.nf` module ([#1875](https://github.com/nf-core/tools/pull/1875)).
 - Check that the workflow name provided with a template doesn't contain dashes ([#1822](https://github.com/nf-core/tools/pull/1822))
-- Remove `CITATION.cff` file from pipeline template, to avoid that pipeline Zenodo entries reference the nf-core publication instead of the pipeline ([#2059](https://github.com/nf-core/tools/pull/2059)).
 
 ### Linting