Releases: Molmed/piper
v1.2.0-beta2
Please note that this is not a stable release!
Major changes
- DNABestPracticeVariantCalling now accepts a xml file which configures the paths to programs and resource files. However all of these paths can also be overridden from the command line if you wish to do so. This approach will be added to all other workflows further down the line, but right now the focus is on getting the DNABestPracticeVariantCalling up to speed to the Swedish Genomes project.
Minor changes
- Better setup instructions.
v1.2.0-beta1
Please note that this is not a stable release! Nonetheless it has a lot of nice things in it, so if you want to try out all the new features, go a head and use it and report any issues back here.
This is the first try out of a large number of features aimed at updating and adapting Piper to be used in the Illumina Genome Network analysis for the Swedish National Genomics Infrastructure. It has a lot of changes to the DNA best practice workflows (both for whole genome and exome analysis), bringing it up to speed with the state of the art tools in the field. But that's not all; the work on the RNA workflows has also begun, and a brand new simplified RNACounts workflow is now available thanks to @Smeds.
Major changes
- GATK updated to 3.1-1-gcfc45fd.
- Variant calling with the GATK Haplotype caller.
- BWA updated to 0.7.5a (and using bwa mem for alignment in the DNA best practice workflows, thus speeding things up considerably).
- Adding qualimap to get summary quality data from DNA alignments.
- A new packing and install procedure using sbt-pack (checkout how to do it in the README).
- A new RNACounts workflow.
- Lot's of changes to the DNABestPractice workflow scripts to make it more modular and support running it only up to certain checkpoints.
Minor changes
- Lot's of legacy stuff has been moved in to special legacy namespaces and will be removed in upcoming releases.
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.