v2 release #136
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v2 release #136
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New container also has updated pysam script with silenced errors.
- paraphase_vcfs now points to a tarball of VCFs; we implemented this change because there is a large, variable number of output VCFs, and we need a flatter output structure
Most changes are internal to the DeepVariant subworkflow, except that custom models should now be passed as a tarball. Instructions are found in the README in `wdl-common/wdl/workflows/deepvariant/README.md`
- singleton, for analyzing single samples; flat input and output structure for better compatibility with platforms like Terra - family, for analyzing families of related samples; still requires a more nested structure for inputs, and outputs are either arrays (for sample-level output) or flat (for joint/tertiary output)
- removed deprecated AWS AGC support - removed hifihla - changed all numerical stats to string representation, because cromwell int representation is out of spec
- providing custom read_pbsv_splits function to read json from file path coerced from string - add container_namespace input to allow ECR URIs to be passed
… top and fixed inputs at bottom.
… top and fixed inputs at bottom.
…nd family workflows.
…d_percent, and added mapped_read_count.
…put. fix: GLnexus joint calling was previously using VCF input instead of gVCF. This has been fixed.
plots: - read length histogram - read quality histogram - aligned depth distribution - alignment MAPQ histogram - alignment gap compressed identity histogram - SNV distribution heatmap - small indel size histogram stats: - many stats added, output both in metadata as well as a flat file workflow metadata: - output workflow_name and workflow_version into metadata
…our private ECR. Documentation to come.
…Omics and DNAnexus.
- updated zenodo doi - updated pbmm2 to 1.16.0 - updated pbsv to 2.10.0 - updated HiFiCNV to 1.0.1 - updated pb-StarPhase to 1.0.1 - updated PharmCat to 2.15.4
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