Merge branch 'dev' into damageprofiler-more

Author: apeltzer

.github/CONTRIBUTING.md

@@ -6,7 +6,9 @@ We try to manage the required tasks for nf-core/eager using GitHub issues, you p
 
 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 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/eager 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/eager, the standard workflow
@@ -30,7 +32,7 @@ Typically, pull-requests are only fully reviewed when these tests are passing, t
 There are typically two types of tests that run:
 
 ### Lint Tests
-The nf-core has a [set of guidelines](http://nf-co.re/developer_docs) which all pipelines must adhere to.
+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.
@@ -42,4 +44,4 @@ 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/eager documentation](https://github.com/nf-core/eager#documentation) and don't hesitate to get in touch on [Gitter](https://gitter.im/nf-core/Lobby)
+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/).

.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

@@ -13,6 +13,7 @@ before_install:
   # Pull the docker image first so the test doesn't wait for this
   - docker pull nfcore/eager: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/eager:dev nfcore/eager:dev
 
 install:
@@ -21,13 +22,16 @@ install:
   - 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 Conda 
   - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
   - bash Miniconda3-latest-Linux-x86_64.sh -b -f -p $HOME/miniconda
   - export PATH="$HOME/miniconda/bin:$PATH"
   # 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:
   - NXF_VER='0.32.0' # Specify a minimum NF version that should be tested and work
@@ -46,6 +50,8 @@ script:
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --skip_trim --saveReference
    # Run the basic pipeline with paired end data without adapterRemoval
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --skip_adapterremoval --saveReference
+   # Run the basic pipeline with output unmapped reads as fastq
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --strip_input_fastq
   # Run the same pipeline testing optional step: fastp, complexity 
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --complexity_filter --bwa_index results/reference_genome/bwa_index/bwa_index/
   # Test BAM Trimming

CHANGELOG.md

@@ -8,14 +8,25 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Added`
 
+* [#189](https://github.com/nf-core/eager/pull/189) - Outputing unmapped reads in a fastq files with the --strip_input_fastq flag
+* [#186](https://github.com/nf-core/eager/pull/186) - Make FastQC skipping [possible]
+/(https://github.com/nf-core/eager/issues/182)
+* Merged in [nf-core/tools](https://github.com/nf-core/tools) release V1.6 template changes  
+
 ### `Fixed`
 * [#152](https://github.com/nf-core/eager/pull/152) - DamageProfiler errors [won't crash entire pipeline anymore](https://github.com/nf-core/eager/issues/171)
 * [#176](https://github.com/nf-core/eager/pull/176) - Increase runtime for DamageProfiler on [large reference genomes](https://github.com/nf-core/eager/issues/173)
+* [#172](https://github.com/nf-core/eager/pull/152) - DamageProfiler errors [won't crash entire pipeline anymore](https://github.com/nf-core/eager/issues/171)
+* [#174](https://github.com/nf-core/eager/pull/190) - Publish DeDup files [properly](https://github.com/nf-core/eager/issues/183) 
 
 ### `Dependencies`
 
 * Added DeDup v0.12.5 (json support)
 * Added mtnucratio v0.5 (json support)
+* Updated Picard 2.18.27 -> 2.19.0
+* Updated GATK 4.1.0.0 -> 4.1.1.1
+* Updated damageprofiler 0.4.4 -> 0.4.5 
+* Updated r-rmarkdown 1.11 -> 1.12
 
 
 ## [2.0.6] - 2019-03-05

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.
 

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018 Alexander Peltzer
+Copyright (c) Alexander Peltzer, Stephen Clayton, James A. Fellows Yates, Maxime Borry
 
 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

@@ -1,14 +1,14 @@
 # ![nf-core/eager](docs/images/eager_logo.png)
 
-[![Build Status](https://travis-ci.org/nf-core/eager.svg?branch=master)](https://travis-ci.org/nf-core/eager)
+**A fully reproducible ancient and modern DNA pipeline in Nextflow and with cloud support.**.
+
+[![Build Status](https://travis-ci.com/nf-core/eager.svg?branch=master)](https://travis-ci.com/nf-core/eager)
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.32.0-brightgreen.svg)](https://www.nextflow.io/)
 [![Slack Status](https://nf-core-invite.herokuapp.com/badge.svg)](https://nf-core-invite.herokuapp.com)[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
 [![Docker Container available](https://img.shields.io/docker/automated/nfcore/eager.svg)](https://hub.docker.com/r/nfcore/eager/)
 ![Singularity Container available](https://img.shields.io/badge/singularity-available-7E4C74.svg)
 [![DOI](https://zenodo.org/badge/135918251.svg)](https://zenodo.org/badge/latestdoi/135918251)
 
-
-
 ## Introduction
 
 **nf-core/eager** is a bioinformatics best-practice analysis pipeline for NGS 
@@ -44,7 +44,7 @@ Additional functionality contained by the pipeline currently includes:
 
 ## Quick Start
 
-1. Install [`nextflow`](docs/installation.md)
+1. Install [`nextflow`](https://nf-co.re/usage/installation)
 
 2. Install one of [`docker`](https://docs.docker.com/engine/installation/), [`singularity`](https://www.sylabs.io/guides/3.0/user-guide/) or [`conda`](https://conda.io/miniconda.html)
 
@@ -73,22 +73,24 @@ as described in the documentation.
 
 ## Documentation
 
-The nf-core/eager pipeline comes with documentation about the pipeline, found in the `docs/` directory:
+The nf-core/eager pipeline comes with documentation about the pipeline, found in the `docs/` directory or on the main homepage of the nf-core project:
 
-1. [Installation](docs/installation.md)
+1. [Nextflow Installation](https://nf-co.re/usage/installation)
 2. Pipeline configuration
-    * [Local installation](docs/configuration/local.md)
-    * [Adding your own system](docs/configuration/adding_your_own.md)
+    * [Pipeline 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)
+6. [EAGER Troubleshooting](docs/troubleshooting.md)
 
 
 ## Credits
 
 This pipeline was written by Alexander Peltzer ([apeltzer](https://github.com/apeltzer)), 
 with major contributions from Stephen Clayton, ideas and documentation from 
-James Fellows Yates, Raphael Eisenhofer and Judith Neukamm. If you want to 
+James A. Fellows Yates, Raphael Eisenhofer, Maxime Borry and Judith Neukamm. If you want to 
 contribute, please open an issue and ask to be added to the project - happy to 
 do so and everyone is welcome to contribute here!
 

Singularity

@@ -5,7 +5,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
-  <meta name="description" content="nf-core/eager: {{ cookiecutter.description }}">
+  <meta name="description" content="nf-core/eager: A fully reproducible ancient and modern DNA pipeline in Nextflow and with cloud support.">
   <title>nf-core/eager Pipeline Report</title>
 </head>
 <body>