bcbio-nextgen v0.6.5 Release Notes
Release Date: 2013-06-07 // almost 11 years ago-
- 👌 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.