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bcbio-nextgen v1.1.0 Release Notes

Release Date: 2018-07-11 // almost 6 years ago
    • Germline calls: rename outputs to samplename-germline to provide easier to understand outputs in final directory.
    • ➕ Add bcbioRNASeq object creation and automatic quality report generation with tools_on: [bcbiornaseq]
    • 👍 CWL: Support germline/somatic calling for tumor samples.
    • CNVkit: improve whole genome runs. Better speed in normalize_sv_coverage through parallelization and avoiding logging. Avoid memory errors in segmentation.
    • UMI: upload prepared UMI bam file (pre-consensus) to final output directory
    • ➕ Add support for bbmap as an aligner
    • RNA-seq variant calling: parallelize GATK HaplotypeCaller over regions to avoid memory and timeout issues.
    • 👌 Support joint calling with GATK using pre-prepared gVCF inputs.
    • RNA-seq variant calling: allow annotation of output variants with vcfanno
    • 👌 Support hg38 builds with peddy QC
    • 👍 QC: support VerifyBamID2 for contamination detection
    • CWL: adjust defaults for align_split_size and nomap_split_targets to match different parallelization and overhead for these runs
    • 👍 CWL: support for Cromwell runner
    • custom genomes: Unzip GTF file prior to installation.
    • Avoid making variant_regions required during processing (by filling with coverage) to differentiate targeted and non analyses downstream.
    • 👍 Avoid attempts to download pre-installed S3 genomes, providing better errors with missing genome installs.
    • Trimming: add explicit polyg option for removing 3' G stretches in NovaSeq and NextSeq data. Now defaults to no polyG trimming unless turned on.
    • Chip-seq: Add RiP calculation for chip-seq data.
    • 👍 DeepVariant and Strelka2 support for customized targeted/genome calling models per region to handle heterogeneous inputs.
    • STAR: enable passing custom options for alignment.
    • Add tools_off: [coverage_qc] option to skip calculating coverage stats (samtools-stats and picard).
    • ➕ Adding BAM file for each sample in small-RNAseq pipeline, samtools and qualimap qc metrics to multiqc report.
    • 👍 Allow arbitrary genomes for ChIP-seq. Thanks to @evchambers for pointing out the issue.