Merge pull request #25 from nf-core/dev

new smrnase release

.github/CONTRIBUTING.md

@@ -0,0 +1,47 @@
+# nf-core/smrnaseq: Contributing Guidelines
+
+Hi there! Many thanks for taking an interest in improving nf-core/smrnaseq.
+
+We try to manage the required tasks for nf-core/smrnaseq 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/smrnaseq 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/smrnaseq, the standard workflow
+is as follows:
+
+1. Check that there isn't already an issue about your idea in the
+   [nf-core/smrnaseq issues](https://github.com/nf-core/smrnaseq/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/smrnaseq repository](https://github.com/nf-core/smrnaseq) 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/smrnaseq documentation](https://github.com/nf-core/smrnaseq#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/smrnaseq: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/smrnaseq!
+
+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/smrnaseq branch on the nf-core/test-datasets repo]( https://github.com/nf-core/test-datasets/pull/new/nf-core/smrnaseq)
+ - [ ] 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/smrnaseq/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

@@ -4,3 +4,4 @@ data/
 results/
 .DS_Store
 tests/test_data
+*.pyc

.travis.yml

@@ -1,38 +1,42 @@
 sudo: required
-language: java
+language: python
 jdk: openjdk8
-services:
-  - docker
-python:
-  - "2.7"
+services: docker
+python: '3.6'
 cache: pip
 matrix:
   fast_finish: true
 
 before_install:
+  # PRs to master are only ok if coming from dev branch
+  - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ])'
   # Pull the docker image first so the test doesn't wait for this
-  - docker pull nfcore/smrnaseq:latest
+  - docker pull nfcore/smrnaseq: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/smrnaseq:dev nfcore/smrnaseq:1.0.0
 
 install:
   # Install Nextflow
-  - mkdir /tmp/nextflow
-  - cd /tmp/nextflow
+  - mkdir /tmp/nextflow && cd /tmp/nextflow
   - wget -qO- get.nextflow.io | bash
   - sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
   # Install nf-core/tools
-  - git clone https://github.com/nf-core/tools.git /tmp/nf-core-tools
-  - cd /tmp/nf-core-tools
-  - pip install --user -e .
+  - pip install --upgrade pip
+  - pip install nf-core
   # Reset
-  - mkdir ${TRAVIS_BUILD_DIR}/tests
-  - cd ${TRAVIS_BUILD_DIR}/tests
+  - mkdir ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
+  # Install markdownlint-cli
+  - sudo apt-get install npm && npm install -g markdownlint-cli
 
 env:
-  - NXF_VER=0.30.2
-  - ''
+  - NXF_VER='0.32.0' # Specify a minimum NF version that should be tested and work
+  - NXF_VER='' # Plus: get the latest NF version and check that it works
 
 script:
   # Lint the pipeline code
   - nf-core lint ${TRAVIS_BUILD_DIR}
-  # Run the pipeline
+  # Lint the documentation
+  - markdownlint ${TRAVIS_BUILD_DIR} -c ${TRAVIS_BUILD_DIR}/.github/markdownlint.yml
+  # Run the pipeline with the test profile
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker

CHANGELOG.md

@@ -1,4 +1,43 @@
-# NGI-smRNAseq
+# nf-core/smrnaseq: Changelog
 
-## [0.1dev](https://github.com/SciLifeLab/NGI-smRNAseq/releases/tag/0.1dev) - 2018-05-14
-* Change bowtie parameters from `bowtie -n x -l 15 -k 10 --best (x=0 for mature and x=1 for hairpin)` into `bowtie -k 1 -m 1 --best --strata`.
+## v1.0.0 - 2019-09-19
+* Add figures to output documentation
+* Add samtools stats for genome alignments
+* Add seqkit and remove razers
+* Add mirtop and razers tools
+* Adapt code and docs to [nf-core](http://nf-co.re/) template
+* Update tools and Dockerfile/Singularity to match current template
+
+#### Dependency Updates
+* openjdk 8.0.144 -> 11.0.1
+* fastqc 0.11.7 -> 0.11.8
+* trim-galore 0.5.0 -> 0.6.2
+* bioconductor-edger 3.20.7 -> 3.26.0
+* bioconductor-limma 3.34.9 -> 3.40.0
+* conda-forge::r-data.table 1.11.4 -> 1.12.2
+* conda-forge::r-gplots 3.0.1 -> 3.0.1.1
+* conda-forge::r-r.methodss3 1.7.1 -> 1.7.1
+* htseq 0.9.1 -> 0.11.2
+* r-markdown 0.9
+* Added mirtop 0.4.18a
+* Removed razers3 3.5.3
+* Added seqkit 0.10.1-1
+* Added seqcluster 1.2.5
+* conda-forge::r-base=3.5.1 -> 3.6.1
+* conda-forge::r-statmod=1.4.30 -> 1.4.32
+* conda-forge::r-markdown=0.9 -> 1.0
+* trim-galore=0.6.2 -> 0.6.3
+* mirtop=0.4.18a -> 0.4.22
+* bioconductor-edger=3.26.0 -> 3.26.5
+* bioconductor-limma=3.40.0 -> 3.40.2
+
+## [1.0](https://github.com/nf-core/smrnaseq/releases/tag/1.0) - 2019-01-10
+* Add "protocol" with pre-defined settings
+* Add miRTrace in the pipeline.
+* Software updates: multiqc 1.6 to 1.7.
+
+## [1.0](https://github.com/nf-core/smrnaseq/releases/tag/1.0) - 2018-08-06
+* Switch from SciLifeLab/NGI-smRNAseq to nf-core/smrnaseq.
+* Use Bowtie 1 instead of Bowtie 2 for the alignment to host reference genome.
+* Add option for sequencing centre in BAM file.
+* Software updates: trim-galore 0.4.5 to 0.5.0; samtools 1.8 to 1.9; multiqc 1.5 to 1.6.

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 +1,7 @@
 FROM nfcore/base
-MAINTAINER Alexander Peltzer <alex.peltzer@gmail.com>
-LABEL authors="alex.peltzer@gmail.com" \
-    description="Docker image containing all requirements for nf-core/smrnaseq pipeline"
+LABEL authors="Alexander Peltzer <alex.peltzer@gmail.com>" \
+      description="Docker image containing all requirements for nf-core/smrnaseq pipeline"
 
 COPY environment.yml /
-RUN conda env update -n root -f /environment.yml && conda clean -a 
+RUN conda env create -f /environment.yml && conda clean -a
+ENV PATH /opt/conda/envs/nf-core-smrnaseq-1.0.0/bin:$PATH

LICENSE.md → LICENSE

@@ -1,6 +1,6 @@
-The MIT License (MIT)
+MIT License
 
-Copyright (c) 2016 chuan-wang
+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