0.7.1 (in progress)

Bug fixes for new approach to parsing *.loc files: handle Galaxy *.loc files with mixed tabs and spaces correctly and fall back to previous approaches when aligner specific *.loc files are missing.
Bug fix for concatenating files when first file in empty.

0.7.0 (July 30, 2013)

RNA-seq pipeline updated: deprecate Tophat 1 in favor of Tophat 2. Perform automatic adapter trimming of common adapter sequences. STAR aligner support. RNA-SeQC support for RNA-seq specific quality control. Transcript quantitation with htseq-count.
Updated installation and upgrade procedures, to make it easier to build an initial analysis pipeline and upgrade bcbio-nextgen and third-parts tools and data in place.
Add support for MuTect tumor/normal variant caller, contributed by Luca Beltrame.
Generalize variant calling to support alternative callers like cancer-specific calling: provide additional associated files to variant calls and pass along sample specific metadata. Document implementation of new variant callers.
Improve algorithms around post-variant calling preparation. Avoid unnecessary tries for VQSR on low coverage whole genome reads, and concatenate VCF files to avoid locking penalties.
Fix logging and memory usage for multicore jobs run within ipython clusters.
Improve logging for IPython cluster issues, including moving IPython logs inside project logging directory for better access.
Options for improved cluster resiliency: minimize number of clusters started during processing with more extensive reuse, flexible timeouts for waiting on cluster start up, and expose options to allow job retries. Thanks to Zhengqiu Cai for suggestions and testing.

Improve logging: Detailed debugging logs collect all process standard out and error and command lines across distributed systems.
Piping improvements: provide fully piped analysis with GATK recalibration and gkno realignment. Handle smaller reads with novoalign piped analysis.
Improve collapsing analysis regions into evenly sized blocks to better handle large numbers of samples analyzed together.
Provide template functionality to ease generation of input sample.yaml files from lists of BAM of fastq files. Thanks to Brent Pedersen and Paul Tang.
Updated program support: Improved novoalign support based on evaluation with reference genomes. Support GATK 2.5-2. Support VarScan 2.3.5.
Fix naming of read group information (ID and SM) to be more robust. Identifies issues with duplicated read groups up front to avoid downstream errors during variant calling. Thanks to Zhengqiu Cai.
Improve quality control metrics: Cleanup into custom qc directory and ensure correct selection of duplicate and other metrics for split post-alignment prep, even without merging.
Fix IPython parallel usage for larger clusters, providing improved resiliency for long running jobs.
Clean up handling of missing programs and input files with better error messages. From Brent Pedersen.

Integrate fully with bcbio.variation to provide automated validation of variant calls against reference materials.
Provide full list of all third party software versions used in analysis.
Create GEMINI database as part of output process, allowing immediate queries of variants with associated population and annotation data.
Collapse analysis regions into evenly sized blocks separated by non-callable regions. Provides better parallelism.
Documentation and examples for NA12878 exome and whole genome pipelines.