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