v1.1.2 - "Boomer"

Major changes

• Changes to adopt Piper to running on the Milou cluster.
• All QScripts now get their settings from the setup xml.
• All the different DNA best practice scripts merged to a single QScript - making the process of running in much smoother, as well as simplifying future development considerably.

Minor changes

• Option to only run alignments in Haloplex workflow.
• Haloplex scripts will do a simple conversion of input files to run on b37 human reference instead of hg19.
• Adding some simple example scripts for demo purposes (to support the Piper workshop).
• ReportParser app added - a simple application to parse report files and extract the number of libraries sequenced and reads passed filter for a sample.
• Improvements to the documentation
• A lot of minor fixes.

v1.1.1 - "Boomer"

Bug fixes

• Fixing Travis CI problems with running tests.

v1.1 - "Boomer"

Major changes

• Changed to the most recent GATK version (2.7-5-g49de937), though this is at the moment checked out from a fork of the GATK (https://github.com/johandahlberg/gatk-protected) as the "jobRunnerJobName" patch (see below) has not been applied to the main GATK branch yet. Later this should be moved back the the main GATK repository.
• The DRMAA job runner now supports the "jobRunnerJobName" field to set the name of the job in the queue. This will hopefully make it easier to handle log parsing in the future. For most jobs it should be set the to something along the lines of projectName + "_my_awesome_job", to make it easier to differentiate between projects in the job queue.
• A tsv format has been provided as an alternative to the report xml's to make it easier to setup Piper with data generated outside the SNP&SEQ Technology platform.
• The script to merge by sample names now hard links files for samples which occur only once.

Bug fixes

• Removing intervals from PrintReads, which caused reads mapped outside of the target area to be dropped.
• Correct Java version in setup
• Lots of small bug fixes

v1.0 - "Helo"

First release of Piper.