bcbio/bcbio-nextgen: v1.2.4

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1.2.4 (21 September 2020) Remove deprecated --genomicsdb-use-vcf-codec option as this is now the default. Add bismark output to MultiQC. Fix PS genotype field from octopus to have the correct type. Edit VarDict headers to report VCFv4.2, since htsjdk does not fully support VCFv4.3 yet. Attempt to speed up bismark by implementing the parallelization strategy suggested here: https://github.com/FelixKrueger/Bismark/issues/96 Add --enumerate option to OptiType to report the top 10 calls and scores, to make it easier to decide how confident we are in a HLA call. Performance improvements when HLA calling during panel sequencing. This skips running bwa-kit during the initial mapping for consensus UMI detection, greatly speeding up panel sequencing runs. Allow custom options to be passed to featureCounts. Fix race condition when running tests. Add TOPMed as a datatarget. Add predicted transcript and peptide output to arriba. Add mm10 as a supported genome for arriba. Skip bcbioRNASeq for more than 100 samples. Add rRNA_pseudogene as a rRNA biotype. Add --genomicsdb-use-vcf-codec when running GenotypeGVCF. See https://gatk.broadinstitute.org/hc/en-us/articles/360040509751- GenotypeGVCFs#--genomicsdb-use-vcf-codec for a discussion. Thanks to @amizeranschi for finding the issue and posting the solution. update VEP to v100 Add consensus peak calling using https://bedops.readthedocs.io/en/latest/content/usage-examples/master-list.html to collapse overlapping peaks. Pre-filter consensus peaks by removing peaks with FDR > 0.05 before performing consensus peak calling. Add support for Qiagen's Qiaseq UPX 3' transcriptome kit for DGE. Support for 96 and 384 well configurations by specifying umi_type: qiagen-upx-96 or umi_type: qiagen-upx-384. Add consensus peak counting using featureCounts. Skip using autosomal-reference when calling ataqv for mouse/human, as this has a problem with ataqv (see https://github.com/ParkerLab/ataqv/issues/10) for discussion and followup. Add pre-generated ataqv HTML report to upload directory. Support single-end reads for ATAC-seq. Move featureCount output files to featureCounts directory in project directory. Remove RNA and reads in peak stats from MultiQC table when they are not calculated for a pipeline. Only show somatic variant counts in the general stats table, if germline variants are calculated. Add kit parameter for setting options for pipelines via just listing the kit. Currently only implemented for WGBS.

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