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Merge pull request #784 from nf-core/dev
v1.12 dev -> master
2 parents 9b3eec9 + d06c16f commit b67fd2a

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‎.github/ISSUE_TEMPLATE/bug_report.md

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---
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name: Bug report
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about: Report something that is broken or incorrect
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labels: bug
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---
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<!--
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# nf-core/tools bug report
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Hi there!
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Thanks for telling us about a problem with the nf-core/tools package.
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Please delete this text and anything that's not relevant from the template below:
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-->
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## Description of the bug
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<!-- A clear and concise description of what the bug is. -->
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## Steps to reproduce
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Steps to reproduce the behaviour:
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1. Command line: <!-- [e.g. `nf-core lint ...`] -->
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2. See error: <!-- [Please provide your error message] -->
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## Expected behaviour
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<!-- A clear and concise description of what you expected to happen. -->
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## System
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- Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->
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- Executor: <!-- [e.g. slurm, local, awsbatch...] -->
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- OS: <!-- [e.g. CentOS Linux, macOS, Linux Mint...] -->
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- Version of nf-core/tools: <!-- [e.g. 1.1, 1.5, 1.8.2...] -->
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- Python version: <!-- [e.g. 3.7, 3.8...] -->
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## Nextflow Installation
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- Version: <!-- [e.g. 19.10.0] -->
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## Additional context
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<!-- Add any other context about the problem here. -->

‎.github/ISSUE_TEMPLATE/config.yml

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blank_issues_enabled: false
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contact_links:
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- name: Join nf-core
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url: https://nf-co.re/join
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about: Please join the nf-core community here
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- name: "Slack #tools channel"
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url: https://nfcore.slack.com/channels/tools
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about: Discussion about the nf-core/tools package

‎.github/ISSUE_TEMPLATE/feature_request.md

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---
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name: Feature request
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about: Suggest an idea for the nf-core website
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labels: enhancement
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---
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<!--
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# nf-core/tools feature request
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Hi there!
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Thanks for suggesting a new feature for the nf-core/tools package!
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Please delete this text and anything that's not relevant from the template below:
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-->
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## Is your feature request related to a problem? Please describe
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<!-- A clear and concise description of what the problem is. -->
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<!-- e.g. [I'm always frustrated when ...] -->
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## Describe the solution you'd like
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<!-- A clear and concise description of what you want to happen. -->
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## Describe alternatives you've considered
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<!-- A clear and concise description of any alternative solutions or features you've considered. -->
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## Additional context
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<!-- Add any other context about the feature request here. -->

‎.github/workflows/branch.yml

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# This workflow is triggered on PRs to master branch on the repository
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# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
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on:
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pull_request:
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pull_request_target:
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branches: [master]
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jobs:
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test:
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runs-on: ubuntu-latest
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steps:
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# PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
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- name: Check PRs
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if: github.repository == 'nf-core/tools'

‎.github/workflows/create-lint-wf.yml

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pip install .
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- name: Install Nextflow
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env:
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CAPSULE_LOG: none
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run: |
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mkdir /tmp/nextflow
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cd /tmp/nextflow

‎.github/workflows/pytest.yml

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env:
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CAPSULE_LOG: none
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mkdir /tmp/nextflow
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cd /tmp/nextflow

‎.github/workflows/sync.yml

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pip install .
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env:
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CAPSULE_LOG: none
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mkdir /tmp/nextflow
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‎CHANGELOG.md

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# nf-core/tools: Changelog
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## [v1.12 - Mercury Weasel](https://github.com/nf-core/tools/releases/tag/1.12) - [2020-11-19]
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### Tools helper code
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* Updated `nf_core` documentation generator for building [https://nf-co.re/tools-docs/](https://nf-co.re/tools-docs/)
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### Template
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* Make CI comments work with PRs from forks [[#765](https://github.com/nf-core/tools/issues/765)]
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* Branch protection and linting results should now show on all PRs
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* Updated GitHub issue templates, which had stopped working
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* Refactored GitHub Actions so that the AWS full-scale tests are triggered after docker build is finished
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* DockerHub push workflow split into two - one for dev, one for releases
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* Updated actions to no longer use `set-env` which is now depreciating [[#739](https://github.com/nf-core/tools/issues/739)]
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* Added config import for `test_full` in `nextflow.config`
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* Switched depreciated `$baseDir` to `$projectDir`
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* Updated minimum Nextflow version to `20.04.10`
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* Make Nextflow installation less verbose in GitHub Actions [[#780](https://github.com/nf-core/tools/pull/780)]
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### Linting
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* Updated code to display colours in GitHub Actions log output
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* Allow tests to pass with `dev` version of nf-core/tools (previous failure due to base image version)
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* Lint code no longer tries to post GitHub PR comments. This is now done in a GitHub Action only.
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## [v1.11 - Iron Tiger](https://github.com/nf-core/tools/releases/tag/1.11) - [2020-10-27]
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### Template

‎README.md

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│ [!] 3 Test Warnings │
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├──────────────────────────────────────────────────────────────────────────────────────────────────────────┤
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│ https://nf-co.re/errors#5: GitHub Actions AWS full test should test full datasets: nf-core-testpipeline… │
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│ https://nf-co.re/errors#8: Conda package is not latest available: bioconda::fastqc=0.11.8, 0.11.9 avail… │
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│ https://nf-co.re/errors#8: Conda package is not latest available: bioconda::multiqc=1.7, 1.9 available │
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│ https://nf-co.re/errors#8: Conda dep outdated: bioconda::fastqc=0.11.8, 0.11.9 available │
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│ https://nf-co.re/errors#8: Conda dep outdated: bioconda::multiqc=1.7, 1.9 available │
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╰──────────────────────────────────────────────────────────────────────────────────────────────────────────╯
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╭───────────────────────╮
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│ LINT RESULTS SUMMARY │

‎docs/api/_src/bump_version.rst

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====================
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.. automodule:: nf_core.bump_version
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:members:
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:members:
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:undoc-members:
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:show-inheritance:
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:private-members:

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