bcbio-nextgen v1.2.5 Release Notes

Release Date: 2021-01-01 // over 1 year ago
    • Joint calling for RNA-seq variant calling requires setting jointcaller to bring it in line with the configuration options for variant calling.
    • ๐Ÿ‘ Allow pre-aligned BAMs and gVCFs for RNA-seq joint variant calling. Thanks to @WimSpree for the feature.
    • ๐Ÿ‘ Allow CollectSequencingArtifacts to be turned off via tools_off: [collectsequencingartifacts].
    • ๐Ÿ›  Fix getiterator -> iter deprecation in ElementTree. Thanks to @smoe.
    • โž• Add SummarizedExperiment object from RNA-seq runs, a simplified version of the bcbioRNASeq object.
    • โž• Add umi_type: dragen. This enables bcbio to run with first-pass, pre-consensus called UMI BAM files from DRAGEN.
    • Turn off inferential replicate loading when creating the gene x sample RNA-seq count matrix. This allows loading of thousands of RNA-seq samples.
    • Only make isoform to gene file from express if we have run express.
    • ๐Ÿ‘ Allow "no consensus peaks found" as a valid endpoint of a ChIP-seq analysis.
    • โœ… Allow BCBIO_TEST_DIR environment variable to control where tests end up.
    • Collect OxoG and other sequencing artifacts due to damage.
    • Round tximport estimated counts.
    • Turn off consensus peak calling for broad peaks. Thanks to @lbeltrame and @LMannarino for diagnosing the broad-peaks-run-forever bug.