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bcbio-nextgen v0.7.7 Release Notes

Release Date: 2014-02-27 // about 10 years ago
    • For cancer tumor/normal calling, attach final call information of both to the tumor sample. This provides a single downstream file for processing and analysis.
    • 📇 Enable batch specification in metadata to be a list, allowing a single normal BAM file to serve as a control for multiple tumor files.
    • Re-organization of parallel framework code to enable alternative approaches. Document plugging in new parallel frameworks. Does not expose changes to users but makes the code cleaner for developers.
    • 0️⃣ Default to 1Gb/core memory usage when not specified in any programs. Do not use default baseline if supplied in input file. Thanks to James Porter.
    • ↔ Integrate plotting of variant evaluation results using prettyplotlib.
    • ➕ Add globals option to configuration to avoid needing to specify the same shared file multiple times in a samples configuration.
    • ✂ Remove deprecated Celery distributed messaging, replaced in favor of IPython.
    • Remove algorithm/custom_algorithm from bcbio_system.yaml, preferring to set these directly in the sample YAML files.
    • ✂ Remove outdated and unused custom B-run trimming.
    • ✂ Remove ability to guess fastq files from directories with no specification in sample YAML. Prefer using generalized template functionality with explicit specification of files in sample YAML file.
    • ✂ Remove deprecated multiplex support, which is outdated and not maintained. Prefer approaches in external tools upstream of bcbio-nextgen.
    • ➕ Add --tag argument which labels job names on a cluster to help distinguish when multiple bcbio jobs run concurrently. Thanks to Jason Corneveaux.
    • Connect min_read_length parameter with read_through trimming in RNA-seq. Thanks to James Porter.
    • Map variant calling specification to variant2 since original approach no longer supported.
    • 🛠 Fix issues with trying to upload directories to Galaxy. Thanks to Jim Peden.
    • Made inner distance calculation for Tophat more accurate.
    • ➕ Added gffutils GFF database to the RNA-seq indices.
    • ➕ Add gene name annotation from the GFF file instead of from mygene.