Merge eca7b53 into d320907

.github/CONTRIBUTING.md

@@ -1,12 +1,14 @@
-# nf-core/rnafusion Contributing Guidelines
+# nf-core/rnafusion: Contributing Guidelines
 
 Hi there! Many thanks for taking an interest in improving nf-core/rnafusion.
 
-We try to manage the required tasks for nf-core/rnafusion using GitHub issues, you probably came to this page when creating one. Please use the prefilled template to save time.
+We try to manage the required tasks for nf-core/rnafusion 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 nf-core/rnafusion then the best place to go is the Gitter chatroom where you can ask us questions directly: https://gitter.im/nf-core/Lobby
+> If you need help using or modifying nf-core/rnafusion 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/rnafusion, the standard workflow
@@ -15,11 +17,31 @@ is as follows:
 1. Check that there isn't already an issue about your idea in the
    [nf-core/rnafusion issues](https://github.com/nf-core/rnafusion/issues) to avoid
    duplicating work.
-    * Feel free to add a new issue here for the same reason.
+    * If there isn't one already, please create one so that others know you're working on this
 2. Fork the [nf-core/rnafusion repository](https://github.com/nf-core/rnafusion) to your GitHub account
 3. Make the necessary changes / additions within your forked repository
-4. Submit a Pull Request against the master branch and wait for the code to be reviewed and merged.
+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/).
 
-For further information/help, please consult the [nf-core/rnafusion documentation](https://github.com/nf-core/rnafusion#documentation) and don't hesitate to get in touch on [Gitter](https://gitter.im/nf-core/Lobby)
+
+## 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/rnafusion documentation](https://github.com/nf-core/rnafusion#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/rnafusion: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.md → .github/PULL_REQUEST_TEMPLATE.md

@@ -5,7 +5,7 @@ Please fill in the appropriate checklist below (delete whatever is not relevant)
 ## 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/rnafusion branch on the nf-core/test-datasets repo]( https://github.com/nf-core/test-datasets/pull/newnf-core/rnafusion)
+ - [ ] If necessary, also make a PR on the [nf-core/rnafusion branch on the nf-core/test-datasets repo]( https://github.com/nf-core/test-datasets/pull/new/nf-core/rnafusion)
  - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
  - [ ] Make sure your code lints (`nf-core lint .`).
  - [ ] Documentation in `docs` is updated

.github/markdownlint.yml

@@ -7,4 +7,3 @@ blanks-around-lists: false
 header-increment: false
 no-duplicate-header:
     siblings_only: true
-no-bare-urls: false # tools only - the {{ jinja variables }} break URLs and cause this to error

.gitignore

@@ -1,5 +1,7 @@
 .nextflow*
 work/
 results/
-tests/
+.DS_Store
+tests/test_data
+*.pyc
 .vscode/

.travis.yml

@@ -1,43 +1,46 @@
 sudo: required
 language: python
+jdk: openjdk8
 services: docker
 python: '3.6'
 cache: pip
 matrix:
   fast_finish: true
 
 before_install:
-  # PRs made to 'master' branch should always orginate from another repo or the 'dev' branch
+  # 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/rnafusion:dev
-  - docker tag nfcore/rnafusion:dev nfcore/rnafusion:1.0.1
-
-env:
-  - 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
+  # 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/rnafusion:dev nfcore/rnafusion:1.0.2
 
 install:
   # Install 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
+  - pip install --upgrade pip
   - pip install nf-core
   # Install markdownlint-cli
   - sudo apt-get install npm && npm install -g markdownlint-cli
-  # Reset 
-  - mkdir ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}
+  # Reset
+  - mkdir ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
+
+env:
+  - 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:
-  # Create and download test data
-  - |
-    touch tests/genome.fa tests/genes.gtf
-    mkdir tests/star_index tests/databases
-    wget https://github.com/nf-core/test-datasets/raw/rnafusion/testdata/human/reads_1.fq.gz -O tests/reads_1.fq.gz
-    wget https://github.com/nf-core/test-datasets/raw/rnafusion/testdata/human/reads_2.fq.gz -O tests/reads_2.fq.gz
   # Lint the pipeline code
   - nf-core lint ${TRAVIS_BUILD_DIR}
-  # Lint markdown
+  # Lint the documentation
   - markdownlint ${TRAVIS_BUILD_DIR} -c ${TRAVIS_BUILD_DIR}/.github/markdownlint.yml
-  # Running the pipeline
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker
+  # Test pipeline help page
+  - nextflow run ${TRAVIS_BUILD_DIR} --help
+  # Test downloading references help page
+  - nextflow run ${TRAVIS_BUILD_DIR}/download-references.nf --help
+  # Test downloading singularity images help page
+  - nextflow run ${TRAVIS_BUILD_DIR}/download-singularity-img.nf --help

CHANGELOG.md

@@ -1,5 +1,17 @@
 # nfcore/rnafusion
 
+## nfcore/rnafusion version 1.0.2 - 2018/05/13
+
+### Changed
+
+* Bumped nf-core template to 1.6 [#69](https://github.com/nf-core/rnafusion/pull/69)
+
+### Fixed
+
+* Fixed COSMIC parameters not wrapped in quotes [#75](https://github.com/nf-core/rnafusion/issues/75)
+* Implemented output output for fusion tools [#72](https://github.com/nf-core/rnafusion/issues/72)
+* Fixed reference download link for STAR-Fusion [#71](https://github.com/nf-core/rnafusion/issues/71)
+
 ## nfcore/rnafusion version 1.0.1 - 2018/04/06
 
 ### Added
@@ -54,4 +66,4 @@ at [SciLifeLab/NGI-RNAfusion](https://github.com/SciLifeLab/NGI-RNAfusion). The
   * STAR-Fusion
   * Fusioncatcher
   * FusionInspector
-  * Custom tool for fusion comparison - generates intersection of detected fusion genes from all tools
+  * Custom tool for fusion comparison - generates intersection of detected fusion genes from all tools

CODE_OF_CONDUCT.md

@@ -34,7 +34,7 @@ This Code of Conduct applies both within project spaces and in public spaces whe
 
 ## Enforcement
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on the [Gitter channel](https://gitter.im/nf-core/Lobby). 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.
+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.
 

Dockerfile

@@ -1,10 +1,7 @@
 FROM nfcore/base
-
-LABEL authors="[email protected], [email protected], [email protected]" \
-    description="Docker image containing all requirements for nfcore/rnafusion pipeline"
+LABEL authors="Martin Proks <[email protected]>" \
+      description="Docker image containing all requirements for nf-core/rnafusion pipeline"
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-rnafusion-1.0.1/bin:$PATH
-
-WORKDIR /
+ENV PATH /opt/conda/envs/nf-core-rnafusion-1.0.2/bin:$PATH

Jenkinsfile

@@ -10,8 +10,7 @@ pipeline {
         stage('Setup environment') {
             steps {
                 sh "pip install nf-core"
-                sh "docker pull nfcore/rnafusion:dev"
-                sh "docker tag nfcore/rnafusion:dev nfcore/rnafusion:1.0.1"
+                sh "docker pull nfcore/rnafusion:1.0.2"
             }
         }
         stage('Lint markdown') {
@@ -22,9 +21,9 @@ pipeline {
         stage('Build') {
             steps {
                 // sh "nextflow run kraken,jenkins nf-core/rnafusion"
-                sh "nextflow run nf-core/rnafusion -r dev --help"
-                sh "nextflow run nf-core/rnafusion/download-references.nf -r dev --help"
-                sh "nextflow run nf-core/rnafusion/download-singularity-img.nf -r dev --help"
+                sh "nextflow run nf-core/rnafusion --help"
+                sh "nextflow run nf-core/rnafusion/download-references.nf --help"
+                sh "nextflow run nf-core/rnafusion/download-singularity-img.nf --help"
             }
         }
     }

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2019 nf-core
+Copyright (c) Rickard Hammarén, Martin Proks
 
 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

@@ -1,5 +1,7 @@
 # ![nf-core/rnafusion](https://raw.githubusercontent.com/nf-core/rnafusion/master/docs/images/rnafusion_logo.png)
 
+**Nextflow rnafusion analysis pipeline, part of the nf-core community.**.
+
 [![Build Status](https://travis-ci.org/nf-core/rnafusion.svg?branch=master)](https://travis-ci.org/nf-core/rnafusion)
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.32.0-brightgreen.svg)](https://www.nextflow.io/)
 [![DOI](https://zenodo.org/badge/151721952.svg)](https://zenodo.org/badge/latestdoi/151721952)
@@ -9,15 +11,9 @@
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
 [![Docker](https://img.shields.io/docker/automated/nfcore/rnafusion.svg)](https://hub.docker.com/r/nfcore/rnafusion)
 
-**nfcore/rnafusion** uses RNA-seq data to detect fusions genes.
-
-The workflow processes RNA-sequencing data from FastQ files. It runs quality control on the raw data ([FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)), detects fusion genes ([STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion), [Fusioncatcher](https://github.com/ndaniel/fusioncatcher), [Ericscript](https://sites.google.com/site/bioericscript/), [Pizzly](https://github.com/pmelsted/pizzly), [Squid](https://github.com/Kingsford-Group/squid)), gathers information ([FusionGDB](https://ccsm.uth.edu/FusionGDB/index.html), [Mitelman](https://cgap.nci.nih.gov/Chromosomes/Mitelman), [COSMIC](https://cancer.sanger.ac.uk/cosmic/fusion)), visualizes the fusions ([FusionInspector](https://github.com/FusionInspector/FusionInspector)), performs quality-control on the results ([MultiQC](http://multiqc.info)) and finally generates custom summary report witch scored fusions ([fusion-report](https://github.com/matq007/fusion-report)).
-
-> Live **demo** output **[here](https://matq007.github.io/fusion-report/example/)**.
-
-The pipeline works with both single-end and paired-end data, though not all fusion detection tools work with single-end data (Ericscript, Pizzly, Squid and FusionInspector).
+## Introduction
 
-The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.
+The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.
 
 | Tool            | Single-end reads | CPU (recommended) | RAM (recommended) |
 | --------------- |:----------------:|:-----------------:|:-----------------:|
@@ -38,14 +34,15 @@ nextflow run nf-core/rnafusion --help
 
 The nf-core/rnafusion pipeline comes with documentation about the pipeline, found in the `docs/` directory:
 
-1. [Installation](docs/installation.md)
+1. [Installation](https://nf-co.re/usage/installation)
 2. Pipeline configuration
     * [Download references for tools](docs/references.md)
-    * [Local installation](docs/configuration/local.md)
-    * [Adding your own system](docs/configuration/adding_your_own.md)
+    * [Local installation](https://nf-co.re/usage/local_installation)
+    * [Adding your own system config](https://nf-co.re/usage/adding_own_config)
+    * [Reference genomes](https://nf-co.re/usage/reference_genomes)
 3. [Running the pipeline](docs/usage.md)
 4. [Output and how to interpret the results](docs/output.md)
-5. [Troubleshooting](docs/troubleshooting.md)
+5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
 
 Use predefined configuration for desired Institution cluster provided at [nfcore/config](https://github.com/nf-core/configs) repository.
 
@@ -65,7 +62,7 @@ bioRxiv 120295; doi: [https://doi.org/10.1101/120295](https://doi.org/10.1101/12
 Páll Melsted, Shannon Hateley, Isaac Charles Joseph, Harold Pimentel, Nicolas L Bray, Lior Pachter, bioRxiv 166322; doi: [https://doi.org/10.1101/166322](https://doi.org/10.1101/166322)
 * **SQUID: transcriptomic structural variation detection from RNA-seq** Cong Ma, Mingfu Shao and Carl Kingsford, Genome Biology, 2018, doi: [https://doi.org/10.1186/s13059-018-1421-5](https://doi.org/10.1186/s13059-018-1421-5)
 * **Fusion-Inspector** download: [https://github.com/FusionInspector](https://github.com/FusionInspector)
-* Martin Proks. (2019, March 26). matq007/fusion-report: **fusion-report:1.0** (Version 1.0). Zenodo. http://doi.org/10.5281/zenodo.2609227
+* Martin Proks. (2019, March 26). matq007/fusion-report: **fusion-report:1.0** (Version 1.0). Zenodo. [http://doi.org/10.5281/zenodo.2609227](http://doi.org/10.5281/zenodo.2609227)
 * **FastQC** download: [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 * **MultiQC** Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. [https://doi.org/10.1093/bioinformatics/btw354](https://doi.org/10.1093/bioinformatics/btw354) Download: [https://multiqc.info/](https://multiqc.info/)