Add CHANGELOG

.travis.yml

@@ -0,0 +1,38 @@
+sudo: required
+language: java
+jdk: openjdk8
+services:
+  - docker
+python:
+  - "2.7"
+cache: pip
+matrix:
+  fast_finish: true
+
+before_install:
+  # Pull the docker image first so the test doesn't wait for this
+  - docker pull nfcore/vipr:latest
+
+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
+  - git clone https://github.com/nf-core/tools.git /tmp/nf-core-tools
+  - cd /tmp/nf-core-tools
+  - pip install --user -e .
+  # Reset
+  - mkdir ${TRAVIS_BUILD_DIR}/tests
+  - cd ${TRAVIS_BUILD_DIR}/tests
+
+env:
+  - NXF_VER=0.31.0 # 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 with the test profile
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker

CHANGELOG.md

@@ -0,0 +1,36 @@
+# 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).
+
+## [Unreleased]
+### `Added`
+  - New ViPR project
+  - Logo
+  - Draft of full documentation and completed Snakemake based testing
+  - [#2](https://github.com/nf-core/vipr/pull/17) - Push container to [nfcore/vipr](https://hub.docker.com/r/nfcore/vipr/)
+  - [#15](https://github.com/nf-core/vipr/issues/15), [#22](https://github.com/nf-core/vipr/pull/22) - This CHANGELOG
+  - [#16](https://github.com/nf-core/vipr/issues/16), [#17](https://github.com/nf-core/vipr/pull/17) - Singularity file
+  - [#22](https://github.com/nf-core/vipr/pull/22) - Enable Travis-CI
+
+### `Changed`
+  - Resource adjustment based on completed FMDV runs
+  - Moved job settings into nextflow.config
+  - nf-core submission
+  - Enhancement to config, run environment and documentation
+  - Adjustments to resource limits after Zika runs and minor cleanup
+
+### `Removed`
+  - [#18](https://github.com/nf-core/vipr/pull/18) Local executor
+  - [#22](https://github.com/nf-core/vipr/pull/22) Institute logos
+
+### `Fixed`
+  - Working and complete version
+  - BAI handling
+  - Capturing special error to be ignored in gap_fill_assembly
+  - pip install in Dockerfile and extended docs
+  - [#11](https://github.com/nf-core/vipr/issues/11), [#14](https://github.com/nf-core/vipr/pull/14) -Font problem in logo
+  - [#12](https://github.com/nf-core/vipr/issues/12), [#14](https://github.com/nf-core/vipr/pull/14) - Remove groovy to close
+  - [#21](https://github.com/nf-core/vipr/pull/21) - Fix containers
+  - [#20](https://github.com/nf-core/vipr/pull/20), [#21](https://github.com/nf-core/vipr/pull/21) - Update documentation

README.md

@@ -6,20 +6,13 @@
 [![Docker Container available](https://img.shields.io/docker/automated/nfcore/vipr.svg)](https://hub.docker.com/r/nfcore/vipr/)
 [![https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg](https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg)](https://singularity-hub.org/collections/1405)
 
-
-
 ### Introduction
 
 **nf-core/vipr** is a bioinformatics best-practice analysis pipeline
 for assembly and intrahost / low-frequency variant calling for viral
 samples.
 
-The pipeline uses [Nextflow](https://www.nextflow.io), a
-bioinformatics workflow tool. It pre-processes raw data from FastQ
-inputs, aligns the reads and performs extensive quality-control on the
-results.
-
-
+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.
 
 ### Pipeline Steps
 
@@ -34,8 +27,6 @@ results.
 | Low frequency variant calling                       | LoFreq                              |
 | Coverage and variant AF plots (two processes)       | Bedtools, ViPR Tools                |
 
-
-
 ### Documentation
 
 Documentation about the pipeline can be found in the `docs/` directory:
@@ -44,14 +35,11 @@ Documentation about the pipeline can be found in the `docs/` directory:
 2. [Running the pipeline](docs/usage.md)
 3. [Output and how to interpret the results](docs/output.md)
 
-
 ### Credits
 
-This pipeline was originally developed at the
-[Genome Institute of Singapore](http://a-star.edu.sg/gis) by
-[Andreas Wilm](https://github.com/andreas-wilm/). It started out as an
-ecosystem around LoFreq an went through a couple of iterations. The
-current version had three predecessors
+This pipeline was originally developed by Andreas Wilm ([andreas-wilm](https://github.com/andreas-wilm)) at [Genome Institute of Singapore](https://www.a-star.edu.sg/gis/).
+It started out as an ecosystem around LoFreq and went through a couple of iterations.
+The current version had three predecessors
 [ViPR 1](https://github.com/CSB5/vipr),
 [ViPR 2](https://github.com/CSB5/vipr2) and
 [ViPR 3](https://github.com/gis-rpd/pipelines/tree/master/germs/vipr)
@@ -68,22 +56,3 @@ Plenty of people provided essential feedback, including:
 - ZHU Yuan
 - Shuzhen SIM
 - CHU Wenhan Collins
-
-### Participating Institutes
-
-nfcore/vipr is used mainly by the Bioinformatics Core of the Genome
-Institue of Singapore. If you use this pipeline too, please let us
-know in an issue and we will add you to the list.
-
-<table>
-  <tr>
-    <td><img src="docs/images/gis_logo.png" width="100"></td>
-    <td>Genome Institute of Singapore</td>
-    <td>https://www.a-star.edu.sg/gis/</td>
-  </tr>
-  <tr>
-    <td><img src="docs/images/igap_logo.png" width="100"></td>
-    <td>iGap</td>
-    <td>http://www.igap.io</td>
-  </tr>
-</table>