Template sync

.github/CONTRIBUTING.md

@@ -0,0 +1,47 @@
+# nf-core/methylseq: Contributing Guidelines
+
+Hi there! Many thanks for taking an interest in improving nf-core/methylseq.
+
+We try to manage the required tasks for nf-core/methylseq 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/methylseq then the best place to ask is on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).
+
+
+
+## Contribution workflow
+If you'd like to write some code for nf-core/methylseq, the standard workflow
+is as follows:
+
+1. Check that there isn't already an issue about your idea in the
+   [nf-core/methylseq issues](https://github.com/nf-core/methylseq/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/methylseq repository](https://github.com/nf-core/methylseq) 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/).
+
+
+## Tests
+When you create a pull request with changes, [Travis CI](https://travis-ci.org/) 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.
+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.
+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.
+
+## Getting help
+For further information/help, please consult the [nf-core/methylseq documentation](https://github.com/nf-core/methylseq#documentation) and don't hesitate to get in touch on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,31 @@
+Hi there!
+
+Thanks for telling us about a problem with the pipeline. Please delete this text and anything that's not relevant from the template below:
+
+#### 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
+A clear and concise description of what you expected to happen.
+
+#### 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. 0.31.0]
+
+#### Container engine:
+ - Engine: [e.g. Conda, Docker or Singularity]
+ - version: [e.g. 1.0.0]
+ - Image tag: [e.g. nfcore/methylseq:1.0.0]
+
+#### Additional context
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,16 @@
+Hi there!
+
+Thanks for suggesting a new feature for the pipeline! Please delete this text and anything that's not relevant from the template below:
+
+#### 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
+A clear and concise description of any alternative solutions or features you've considered.
+
+#### Additional context
+Add any other context about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,15 @@
+Many thanks to contributing to nf-core/methylseq!
+
+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/methylseq branch on the nf-core/test-datasets repo]( https://github.com/nf-core/test-datasets/pull/new/nf-core/methylseq)
+ - [ ] 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/methylseq/tree/master/.github/CONTRIBUTING.md

.github/markdownlint.yml

@@ -0,0 +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

.gitignore

@@ -2,5 +2,6 @@
 work/
 data/
 results/
-tests/test_data/ngi-bisulfite_test_set/
 .DS_Store
+tests/test_data
+*.pyc

.travis.yml

@@ -13,6 +13,7 @@ before_install:
   # Pull the docker image first so the test doesn't wait for this
   - docker pull nfcore/methylseq:dev
   # Fake the tag locally so that the pipeline runs properly
+  # Looks weird when this is :dev to :dev, but makes sense when testing code for a release (:dev to :1.0.1)
   - docker tag nfcore/methylseq:dev nfcore/methylseq:dev
 
 install:
@@ -25,7 +26,9 @@ install:
   - pip install nf-core
   # Reset
   - mkdir ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
-
+  # Install markdownlint-cli
+  - sudo apt-get install npm && npm install -g markdownlint-cli
+
 env:
   - ALIGNER=bismark ALIGNER_REF="--bismark_index ${TRAVIS_BUILD_DIR}/tests/results/reference_genome/BismarkIndex/" NXF_VER='0.32.0'
   - ALIGNER=bismark ALIGNER_REF="--bismark_index ${TRAVIS_BUILD_DIR}/tests/results/reference_genome/BismarkIndex/"
@@ -37,6 +40,8 @@ env:
 script:
   # Lint the pipeline code
   - nf-core lint ${TRAVIS_BUILD_DIR}
+  # Lint the documentation
+  - markdownlint ${TRAVIS_BUILD_DIR} -c ${TRAVIS_BUILD_DIR}/.github/markdownlint.yml
   # Run, build reference genome
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --aligner $ALIGNER --saveReference
   # Basic run with supplied reference

CHANGELOG.md

@@ -11,11 +11,17 @@
 * Added `--methylKit` option to run MethylDackel with the `--methylKit` flag, producing output suitable for the methylKit R package.
 
 #### Software updates
-* bismark `0.20.0` > `0.21.0`
-* _new dependency_: hisat2 `2.1.0` 
+* _new dependency_: hisat2 `2.1.0`
+* _new dependency_: r-markdown `0.9`
+* Bismark `0.20.0` > `0.22.1`
+* Bowtie2 `2.3.4.3` > `2.3.5`
+* Picard `2.18.21` > `2.19.1`
+* MethylDackel `0.3.0` > `0.4.0`
+
 
 #### Pipeline updates
 * Changed `params.container` for `process.container`
+* Merged TEMPLATE branch
 
 
 
@@ -59,19 +65,19 @@
 ## [v1.1](https://github.com/nf-core/methylseq/releases/tag/1.1) - 2018-08-09
 
 * Tests simplified - now work by simply using the `test` config profile
-    * eg: `nextflow run nf-core/methylseq -profile test,docker`
-    * Removed previous `run_test.sh` script and data
+  * eg: `nextflow run nf-core/methylseq -profile test,docker`
+  * Removed previous `run_test.sh` script and data
 * New `Singularity` build script for direct compatibility with [singularity-hub](https://singularity-hub.org/)
 * Minor improvements to the docs
 * A number of boilerplate nf-core code updates
 * Updated `process$name` nextflow syntax to avoid warnings in new versions of nextflow
 * Updated software tools
-    * `trim-galore` `v0.4.5` update to `0.5.0`
-    * `samtools` `v1.8` update to `1.9`
-    * `bowtie2` `v2.3.4.1` update to `2.3.4.2`
-    * `multiqc` `v1.5` update to `1.6`
-    * `picard` `v2.18.2` update to `2.18.11`
-    * `bwameth` `v0.2.0` update to `0.2.2`
+  * `trim-galore` `v0.4.5` update to `0.5.0`
+  * `samtools` `v1.8` update to `1.9`
+  * `bowtie2` `v2.3.4.1` update to `2.3.4.2`
+  * `multiqc` `v1.5` update to `1.6`
+  * `picard` `v2.18.2` update to `2.18.11`
+  * `bwameth` `v0.2.0` update to `0.2.2`
 
 
 

CODE_OF_CONDUCT.md

@@ -0,0 +1,46 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on [Slack](https://nf-core-invite.herokuapp.com/). The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

Dockerfile

@@ -1,7 +1,6 @@
 FROM nfcore/base
-MAINTAINER Phil Ewels <phil.ewels@scilifelab.se>
 LABEL authors="phil.ewels@scilifelab.se" \
-    description="Container image containing all requirements for the nf-core/methylseq pipeline"
+    description="Docker image containing all requirements for the nf-core/methylseq pipeline"
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a

LICENCE.md → LICENSE

@@ -1,6 +1,6 @@
-The MIT License (MIT)
+MIT License
 
-Copyright (c) Phil Ewels
+Copyright (c) Phil Ewels <phil.ewels@scilifelab.se>
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -37,7 +37,7 @@ Choose between workflows by using `--aligner bismark` (default, uses bowtie2 for
 ### Documentation
 The nf-core/methylseq pipeline comes with documentation about the pipeline, found in the `docs/` directory:
 
-1. [Installation and configuration](docs/installation.md)
+1. [Installation](https://nf-co.re/usage/installation)
 2. [Running the pipeline](docs/usage.md)
 3. [Output and how to interpret the results](docs/output.md)
 

assets/email_template.html

@@ -10,18 +10,10 @@
 <body>
 <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
 
-<img src="cid:ngimethylseqlogo">
-
-<h1>nf-core/methylseq: Bisulfite-Seq Best Practice v${version}</h1>
+<h1>nf-core/methylseq v${version}</h1>
 <h2>Run Name: $runName</h2>
 
-<% if (success){
-    out << """
-    <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        nf-core/methylseq execution completed successfully!
-    </div>
-    """
-} else {
+<% if (!success){
     out << """
     <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
         <h4 style="margin-top:0; color: inherit;">nf-core/methylseq execution completed unsuccessfully!</h4>
@@ -30,6 +22,12 @@ <h4 style="margin-top:0; color: inherit;">nf-core/methylseq execution completed
         <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
     </div>
     """
+} else {
+    out << """
+    <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+        nf-core/methylseq execution completed successfully!
+    </div>
+    """
 }
 %>
 
@@ -44,15 +42,8 @@ <h3>Pipeline Configuration:</h3>
     </tbody>
 </table>
 
-<p>nf-core/methylseq is a bioinformatics best-practice analysis pipeline used for Methylation (BS-Seq) data analysis at the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden.</p>
-<p>The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.</p>
-<p>For more information, please see the pipeline homepage: <a href="https://github.com/nf-core/methylseq">https://github.com/nf-core/methylseq</a></p>
-
-<hr style="height: 3px; padding: 0; margin: 24px 0; background-color: #e1e4e8; border: 0;">
-
-<img src="cid:scilifelablogo">
-<img src="cid:ngilogo">
-
+<p>nf-core/methylseq</p>
+<p><a href="https://github.com/nf-core/methylseq">https://github.com/nf-core/methylseq</a></p>
 
 </div>
 

assets/email_template.txt

@@ -1,6 +1,9 @@
-=================================================
  nf-core/methylseq: Bisulfite-Seq Best Practice v${version}
 =================================================
+=======
+========================================
+ nf-core/methylseq v${version}
+========================================
 Run Name: $runName
 
 <% if (success){
@@ -28,7 +31,5 @@ Pipeline Configuration:
 <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %>
 
 --
-nf-core/methylseq is a bioinformatics best-practice analysis pipeline used for Methylation (BS-Seq) data analysis at the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden.
-The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
-For more information, please see the pipeline homepage: https://github.com/nf-core/methylseq
-
+nf-core/methylseq
+https://github.com/nf-core/methylseq

conf/multiqc_config.yaml → assets/multiqc_config.yaml

@@ -12,3 +12,4 @@ table_columns_visible:
         percentage_aligned: false
 top_modules:
     - 'bismark'
+export_plots: true