- CSS calling and demultiplexing with Lima have been removed from the pipeline. PacBio-variantcalling now expects one or more post-CCS bam files per sample, and only performs variantcalling.
- Allow nested inputs for better control over individual jobs.
- Fix bug in MultiQC pbmarkdup module for long library names.
- Add VCF Metrics to MultiQC report (only used when VariantCalling.dbsnp is specified).
- Include pbmarkdup in pipeline.
- Upgrade MultiQC_PGx to latest version.
- Update documentation and add conda environment file.
- Dummy release for Zenodo.
- Move pipeline out of BioWDL.
- Make g.vcf output optional, because generating a g.vcf with DeepVariant is extremely slow. This changes the default behaviour.
- Set scatter size for GATK and DeepVariant to 350 million basepairs.
- Add scattering to the genotyping steps for GATK and DeepVariant.
- Automatically convert target and bait bed files to picard .interval files, simplifying the output.
- Add custom MultiQC configuration file.
- Update tasks and the input/output names.