bcbio/bcbio-nextgen: v1.2.5

1.2.5 (01 January 2021)

• Joint calling for RNA-seq variant calling requires setting jointcaller to bring it in line with the configuration options for variant calling.
• Allow pre-aligned BAMs and gVCFs for RNA-seq joint variant calling. Thanks to @WimSpree for the feature.
• Allow CollectSequencingArtifacts to be turned off via tools_off: [collectsequencingartifacts].
• Fix getiterator -> iter deprecation in ElementTree. Thanks to @smoe.
• Add SummarizedExperiment object from RNA-seq runs, a simplified version of the bcbioRNASeq object.
• 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.
• Allow "no consensus peaks found" as a valid endpoint of a ChIP-seq analysis.
• 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.