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bcbio-nextgen v0.7.2 Release Notes

Release Date: 2013-08-30 // over 10 years ago
    • ⏱ Report memory usage for processes to cluster schedulers and use predicted memory usage to schedule cores per machine. Gets core and memory information for machines and uses to ensure submitted jobs can schedule with available resources.
    • 🔧 Provide error checking of input YAML configuration at run start. Avoids accidental typos or incorrect settings that won't error out until later in the process.
    • Drop requirement for fc_name and fc_date in input YAML file. Individual sample names are instead used and required to be unique within a processing run.
    • ✂ Remove original variant pipeline, replacing with the all around better variant2 analysis method. Plan for the next version is to automatically redirect to variant2.
    • 👌 Improve parallelization of BAM preparation and gemini database creation by moving to multicore versions.
    • 🚚 Move variant annotation to work on called sub-regions, to avoid bottlenecks when annotating a full whole genome VCF.
    • ✂ Remove sequencer-specific integration functionality which is poorly maintained and better done with third party tools: demultiplexing and statistics from Illumina directories.
    • 🐛 Bug fix to re-enable template generation functionality.
    • 👌 Improve BAM merging on large files using samtools for output sort.
    • Uploading results works with the RNA-seq pipeline.
    • Rework internals to provide a consistent dictionary of sample attributes up front, avoiding lane/sample dichotomy which provided confusing internal code.
    • ⬇️ Drop calling htseq-count from the command line in favor of an internal implementation.