- Automatically calculate `coverage_interval` based on coverage calculations,
avoiding need to set this directly in input configuration.
- Update vt decompose to handle additional multi-allelic adjustments including
all format attributes, providing full support for new GEMINI changes. Thanks
to Brent Pedersen and Adrian Tan.
- Add `default` configuration target to `bcbio_system.yaml` reducing the need
to set program specific arguments for everything.
- Ensure `resources` specified in input YAML get passed to global system
configuration for making parallelization decisions. Thanks to Miika Ahdesmaki.
- Run upload process on distributed machines, allowing upload to S3 on AWS to take
advantage of machines with multiple cores. Thanks to Lorena Pantano.
- Re-write interactions with external object stores like S3 to be more general
and incorporate multiple regions and future support for non-S3 storage.
- Scale local jobs by total memory usage when memory constrains resource usage
jinstead of cores. Thanks to Sven-Eric Schelhorn and Lorena Pantano.
- Disambiguation: improve parallelization by disambiguating on split alignment
parts prior to merging. Thanks to Sven-Eric Schelhorn.
- Disambiguation: ensure ambiguous and other organism reads are sorted, merged
and passed to final upload directory. Thanks to Sven-Eric Schelhorn.
- Fix problem with sambamba name sorting not being compatible with samtools.
Thanks to Sven-Eric Schelhorn.
- FreeBayes: update to latest version (0.9.21-7) with validation
(http://imgur.com/a/ancGz).
- Allow bz2 files in bcbio_prepare_sample.py script.
- Ensure GEMINI statistics run for project summary file. Thanks to Luca
Beltrame.
- Better error checking for booleans in input configuration. Thanks to Daryl
Waggott.
- Implement qualimap for RNAseq QC metrics, but not active yet.
- collect statistics graphing capabilities moved from bcbio-nextgen-vm, enabling
plotting of resource usage during runs. Thanks to John Morrissey and Lorena
Pantano.