Merge pull request #363 from nf-core/dev

Pull request for release of 2.1.0

.github/CONTRIBUTING.md

@@ -1,47 +1,57 @@
 # nf-core/eager: Contributing Guidelines
 
-Hi there! Many thanks for taking an interest in improving nf-core/eager.
+Hi there!
+Many thanks for taking an interest in improving nf-core/eager.
 
-We try to manage the required tasks for nf-core/eager using GitHub issues, you probably came to this page when creating one. Please use the pre-filled template to save time.
-
-However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;)
-
-> If you need help using or modifying nf-core/eager then the best place to ask is on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).
+We try to manage the required tasks for nf-core/eager using GitHub issues, you probably came to this page when creating one.
+Please use the pre-filled template to save time.
 
+However, don't be put off by this template - other more general issues and suggestions are welcome!
+Contributions to the code are even more welcome ;)
 
+> If you need help using or modifying nf-core/eager then the best place to ask is on the nf-core Slack [#eager](https://nfcore.slack.com/channels/eager) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Contribution workflow
-If you'd like to write some code for nf-core/eager, the standard workflow
-is as follows:
 
-1. Check that there isn't already an issue about your idea in the
-   [nf-core/eager issues](https://github.com/nf-core/eager/issues) to avoid
-   duplicating work.
+If you'd like to write some code for nf-core/eager, the standard workflow is as follows:
+
+1. Check that there isn't already an issue about your idea in the [nf-core/eager issues](https://github.com/nf-core/eager/issues) to avoid duplicating work
     * If there isn't one already, please create one so that others know you're working on this
-2. Fork the [nf-core/eager repository](https://github.com/nf-core/eager) to your GitHub account
+2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/eager repository](https://github.com/nf-core/eager) to your GitHub account
 3. Make the necessary changes / additions within your forked repository
-4. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged.
-
-If you're not used to this workflow with git, you can start with some [basic docs from GitHub](https://help.github.com/articles/fork-a-repo/) or even their [excellent interactive tutorial](https://try.github.io/).
+4. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
 
+If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
 
 ## Tests
-When you create a pull request with changes, [Travis CI](https://travis-ci.org/) will run automatic tests.
+
+When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
 
 There are typically two types of tests that run:
 
 ### Lint Tests
-The nf-core has a [set of guidelines](http://nf-co.re/guidelines) which all pipelines must adhere to.
+
+`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
 To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
 
 If any failures or warnings are encountered, please follow the listed URL for more documentation.
 
 ### Pipeline Tests
-Each nf-core pipeline should be set up with a minimal set of test-data.
-Travis CI then runs the pipeline on this data to ensure that it exists successfully.
+
+Each `nf-core` pipeline should be set up with a minimal set of test-data.
+`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
 If there are any failures then the automated tests fail.
-These tests are run both with the latest available version of Nextflow and also the minimum required version that is stated in the pipeline code.
+These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code.
+
+## Patch
+
+: warning: Only in the unlikely and regretful event of a release happening with a bug.
+
+* On your own fork, make a new branch `patch` based on `upstream/master`.
+* Fix the bug, and bump version (X.Y.Z+1).
+* A PR should be made on `master` from patch to directly this particular bug.
 
 ## Getting help
-For further information/help, please consult the [nf-core/eager documentation](https://github.com/nf-core/eager#documentation) and don't hesitate to get in touch on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).
+
+For further information/help, please consult the [nf-core/eager documentation](https://nf-co.re/nf-core/eager/docs) and don't hesitate to get in touch on the nf-core Slack [#eager](https://nfcore.slack.com/channels/eager) channel ([join our Slack here](https://nf-co.re/join/slack)).

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,27 +1,42 @@
----
-name: Bug report
-about: Create a report to help us improve
+# nf-core/eager bug report
 
----
+Hi there!
 
-**Describe the bug**
-A clear and concise description of what the bug is. What does not work and what did you do to produce a problem?
+Thanks for telling us about a problem with the pipeline.
+Please delete this text and anything that's not relevant from the template below:
 
-**To Reproduce**
-Steps to make me able to reproduce the behavior:
-1. Run the pipeline with parameters X
-2. Describe your input data: What did you provide as input? Ideally, you could send me a parameter file + your input data or at least tell me what the latter looks like.
+## Describe the bug
+
+A clear and concise description of what the bug is.
+
+## Steps to reproduce
+
+Steps to reproduce the behaviour:
+
+1. Command line: `nextflow run ...`
+2. See error: _Please provide your error message_
+
+## Expected behaviour
 
-**Expected behavior**
 A clear and concise description of what you expected to happen.
 
-**Screenshots**
-If applicable, add screenshots to help explain your problem.
+## System
+
+- Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->
+- Executor: <!-- [e.g. slurm, local, awsbatch...] -->
+- OS: <!-- [e.g. CentOS Linux, macOS, Linux Mint...] -->
+- Version <!-- [e.g. 7, 10.13.6, 18.3...] -->
+
+## Nextflow Installation
+
+- Version: <!-- [e.g. 19.10.0] -->
+
+## Container engine
+
+- Engine: <!-- [e.g. Conda, Docker or Singularity] -->
+- version: <!-- [e.g. 2.1.0] -->
+- Image tag: <!-- [e.g. nfcore/eager:2.1.0] -->
 
-**Operating System:**
- - OS: [e.g. which Linux did you use?]
+## Additional context
 
-**Additional context**
-Please provide me with the following files:
-- `.nextflow.log`
-- `results/pipeline_info/...`
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,17 +1,24 @@
----
-name: Feature request
-about: Suggest an idea for this project
+# nf-core/eager feature request
 
----
+Hi there!
 
-**Is your feature request related to a problem? Please describe.**
-A clear and concise description of what the problem is. Example: I always need to extract unmapped reads from a BAM file after the pipeline run.
+Thanks for suggesting a new feature for the pipeline!
+Please delete this text and anything that's not relevant from the template below:
 
-**Describe the solution you'd like**
-A clear and concise description of what you want to happen. Example: Could you maybe add an option to extract unmapped reads directly after mapping to FastQ format so I can map these using a different method? 
+## Is your feature request related to a problem? Please describe
+
+A clear and concise description of what the problem is.
+
+Ex. I'm always frustrated when [...]
+
+## Describe the solution you'd like
+
+A clear and concise description of what you want to happen.
+
+## Describe alternatives you've considered
 
-**Describe alternatives you've considered**
 A clear and concise description of any alternative solutions or features you've considered.
 
-**Additional context**
-Add any other context or screenshots about the feature request here.
+## Additional context
+
+Add any other context about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,15 +1,19 @@
-Many thanks to contributing to nf-core/eager!
+# nf-core/eager pull request
 
-Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).
+Many thanks for contributing to nf-core/eager!
+
+Please fill in the appropriate checklist below (delete whatever is not relevant).
+These are the most common things requested on pull requests (PRs).
 
 ## PR checklist
- - [ ] This comment contains a description of changes (with reason)
- - [ ] If you've fixed a bug or added code that should be tested, add tests!
- - [ ] If necessary, also make a PR on the [nf-core/eager branch on the nf-core/test-datasets repo]( https://github.com/nf-core/test-datasets/pull/new/nf-core/eager)
- - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
- - [ ] Make sure your code lints (`nf-core lint .`).
- - [ ] Documentation in `docs` is updated
- - [ ] `CHANGELOG.md` is updated
- - [ ] `README.md` is updated
-
-**Learn more about contributing:** https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md
+
+- [ ] This comment contains a description of changes (with reason)
+- [ ] If you've fixed a bug or added code that should be tested, add tests!
+- [ ] If necessary, also make a PR on the [nf-core/eager branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/eager)
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --paired_end`).
+- [ ] Make sure your code lints ([`nf-core lint .`](https://nf-co.re/tools)).
+- [ ] Documentation in `docs` is updated
+- [ ] `CHANGELOG.md` is updated
+- [ ] `README.md` is updated
+
+**Learn more about contributing:** [CONTRIBUTING.md](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)

.github/PULL_REQUEST_TEMPLATE/pull_request_template.md

@@ -0,0 +1,18 @@
+Many thanks to contributing to nf-core/eager!
+
+Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).
+
+## PR checklist
+
+ - [ ] This comment contains a description of changes (with reason).
+ - [ ] If you've fixed a bug or added code that should be tested, add tests!
+   - [ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py`
+   - [ ] If necessary, also make a PR on the [nf-core/eager branch on the nf-core/test-datasets repo]( https://github.com/nf-core/test-datasets/pull/new/nf-core/eager).
+ - [ ] Make sure your code lints (`nf-core lint .`).
+ - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
+ - [ ] Usage Documentation in `docs/usage.md` is updated.
+ - [ ] Output Documentation in `docs/output.md` is updated.
+ - [ ] `CHANGELOG.md` is updated.
+ - [ ] `README.md` is updated (including new tool citations and authors/contributors).
+
+**Learn more about contributing:** https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md

.github/markdownlint.yml

@@ -1,9 +1,9 @@
 # Markdownlint configuration file
 default: true,
 line-length: false
-no-multiple-blanks: 0
-blanks-around-headers: false
-blanks-around-lists: false
-header-increment: false
 no-duplicate-header:
     siblings_only: true
+no-inline-html: 
+    allowed_elements:
+        - img
+        - p

.github/workflows/branch.yml

@@ -0,0 +1,16 @@
+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`
+on:
+  pull_request:
+    branches:
+    - master
+
+jobs:
+  test:
+    runs-on: ubuntu-18.04
+    steps:
+      # PRs are only ok if coming from an nf-core `dev` branch or a fork `patch` branch
+      - name: Check PRs
+        run: |
+          { [[ $(git remote get-url origin) == *nf-core/eager ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == "patch" ]]