Merge pull request #223 from nf-core/dev

PR for 2.0.7 release - please merge ASAP

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

@@ -13,21 +13,25 @@ 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
-  - docker tag nfcore/eager:dev nfcore/eager:2.0.6
+  # 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:2.0.7
 
 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 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
@@ -38,23 +42,32 @@ script:
   - nf-core lint ${TRAVIS_BUILD_DIR}
   # Run the basic pipeline with the test profile
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --saveReference
+  # Test using PMD tools
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --run_pmdtools --pairedEnd
   # Run the basic pipeline with single end data (pretending its single end actually)
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --singleEnd --bwa_index results/reference_genome/bwa_index/bwa_index/
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --singleEnd --bwa_index results/reference_genome/bwa_index/BWAIndex/Mammoth_MT_Krause.fasta
   # Run the basic pipeline with paired end data without collapsing
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --skip_collapse --saveReference
   # Run the basic pipeline with paired end data without trimming
   - 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/
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --complexity_filter --bwa_index results/reference_genome/bwa_index/BWAIndex/Mammoth_MT_Krause.fasta
   # Test BAM Trimming
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --trim_bam --bwa_index results/reference_genome/bwa_index/bwa_index/
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --trim_bam --bwa_index results/reference_genome/bwa_index/BWAIndex/Mammoth_MT_Krause.fasta
   # Test running with CircularMapper
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --circularmapper --circulartarget 'NC_007596.2'
   # Test running with BWA Mem
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --bwamem --bwa_index results/reference_genome/bwa_index/bwa_index/
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --bwamem --bwa_index results/reference_genome/bwa_index/BWAIndex/Mammoth_MT_Krause.fasta
   # Test with zipped reference input
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --fasta 'https://raw.githubusercontent.com/nf-core/test-datasets/eager2/reference/Test.fasta.gz'
   # Run the basic pipeline with the bam input profile
   - nextflow run ${TRAVIS_BUILD_DIR} -profile testbam,docker --bam
+  # Run the basic pipeline with FastA reference with `fna` extension
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test_fna,docker --pairedEnd --saveReference
+  # Test using pre-computed indices from a separate run beforehand
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test_fna,docker --pairedEnd --bwa_index results/reference_genome/bwa_index/BWAIndex/Mammoth_MT_Krause.fna --fasta_index results/reference_genome/fasta_index/Mammoth_MT_Krause.fna.fai --seq_dict results/reference_genome/seq_dict/Mammoth_MT_Krause.dict 
+

CHANGELOG.md

@@ -1,9 +1,45 @@
 # nf-core/eager: Changelog
+
 All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## [2.0.7] - 2019-06-10
+
+### `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  
+* A lot more automated tests using Travis CI
+* Don't ignore DamageProfiler errors anymore 
+* [#220](https://github.com/nf-core/eager/pull/220) - Added post-mapping filtering statistics module and corresponding MultiQC statistics [#217](https://github.com/nf-core/eager/issues/217)
+
+### `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)
+* [#196](https://github.com/nf-core/eager/pull/196) - Fix reference [issues](https://github.com/nf-core/eager/issues/150)
+* [#196](https://github.com/nf-core/eager/pull/196) - Fix issues with PE data being mapped incompletely
+* [#200](https://github.com/nf-core/eager/pull/200) - Fix minor issue with some [typos](https://github.com/nf-core/eager/pull/196)
+* [#210](https://github.com/nf-core/eager/pull/210) - Fix PMDTools [encoding issue](https://github.com/pontussk/PMDtools/issues/6) from `samtools calmd` generated files by running through `sa]mtools view` first
+* [#221](https://github.com/nf-core/eager/pull/221) - Fix BWA Index [not being reused by multiple samples](https://github.com/nf-core/eager/issues/219)
+
+### `Dependencies`
+
+* Added DeDup v0.12.5 (json support)
+* Added mtnucratio v0.5 (json support)
+* Updated Picard 2.18.27 -> 2.20.2
+* Updated GATK 4.1.0.0 -> 4.1.2.0
+* Updated damageprofiler 0.4.4 -> 0.4.5
+* Updated r-rmarkdown 1.11 -> 1.12
+* Updated fastp 0.19.7 -> 0.20.0
+* Updated qualimap 2.2.2b -> 2.2.2c
+
 ## [2.0.6] - 2019-03-05
 
 ### `Added`
@@ -19,28 +55,33 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * [#145](https://github.com/nf-core/eager/pull/145) - Added Picard Memory Handling [fix](https://github.com/nf-core/eager/issues/144)
 
 ### `Dependencies`
+
 * Picard Tools 2.18.23 -> 2.18.27
 * GATK 4.0.12.0 -> 4.1.0.0
 * FastP 0.19.6 -> 0.19.7
 
 ## [2.0.5] - 2019-01-28
 
 ### `Added`
+
 * [#127](https://github.com/nf-core/eager/pull/127) - Added a second testcase for testing the pipeline properly
 * [#129](https://github.com/nf-core/eager/pull/129) - Support BAM files as [input format](https://github.com/nf-core/eager/issues/41)
 * [#131](https://github.com/nf-core/eager/pull/131) - Support different [reference genome file extensions](https://github.com/nf-core/eager/issues/130)
 
 ### `Fixed`
+
 * [#128](https://github.com/nf-core/eager/issues/128) - Fixed reference genome handling errors
 
 ### `Dependencies`
+
 * Picard Tools 2.18.21 -> 2.18.23
 * R-Markdown 1.10 -> 1.11
 * FastP 0.19.5 -> 0.19.6
 
 ## [2.0.4] - 2019-01-09
 
 ### `Added`
+
 * [#111](https://github.com/nf-core/eager/pull/110) - Allow [Zipped FastA reference input](https://github.com/nf-core/eager/issues/91)
 * [#113](https://github.com/nf-core/eager/pull/113) - All files are now staged via channels, which is considered best practice by Nextflow 
 * [#114](https://github.com/nf-core/eager/pull/113) - Add proper runtime defaults for multiple processes 
@@ -55,27 +96,33 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ## [2.0.3] - 2018-12-12
 
 ### `Added`
+
 * [#80](https://github.com/nf-core/eager/pull/80) - BWA Index file handling 
 * [#77](https://github.com/nf-core/eager/pull/77) - Lots of documentation updates by [@jfy133](https://github.com/jfy133)
 * [#81](https://github.com/nf-core/eager/pull/81) - Renaming of certain BAM options
 * [#92](https://github.com/nf-core/eager/issues/92) - Complete restructure of BAM options
 
 ### `Fixed`
+
 * [#84](https://github.com/nf-core/eager/pull/85) - Fix for [Samtools index issues](https://github.com/nf-core/eager/issues/84)
 * [#96](https://github.com/nf-core/eager/issues/96) - Fix for [MarkDuplicates issues](https://github.com/nf-core/eager/issues/96) found by [@nilesh-tawari](https://github.com/nilesh-tawari)
 
 ### Other
+
 * Added Slack button to repository readme
 
 ## [2.0.2] - 2018-11-03
 
 ### `Changed`
+
 * [#70](https://github.com/nf-core/eager/issues/70) - Uninitialized `readPaths` warning removed
 
 ### `Added`
+
 * [#73](https://github.com/nf-core/eager/pull/73) - Travis CI Testing of Conda Environment added 
 
 ### `Fixed`
+
 * [#72](https://github.com/nf-core/eager/issues/72) - iconv Issue with R in conda environment
 
 ## [2.0.1] - 2018-11-02

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

@@ -3,4 +3,4 @@ FROM nfcore/base
 LABEL description="Docker image containing all requirements for nf-core/eager pipeline"
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-eager-2.0.6/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.0.7/bin:$PATH

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!