- UMI deduplication stats collection is now optional.
- Added umi based deduplication.
- Added an overview of all inputs to the docs.
- Added parameter_meta.
- Added wdl-aid to linting.
- Update QC submodule to latest version.
- Added miniwdl to linting.
- Update tasks so they pass the correct memory requirements to the execution engine. Memory requirements are set on a per-task (not per-core) basis.
- Allow using csv table format samplesheet as input format.
- Update cutadapt version to 2.4
- Allow more than one gtf/gff file for annotation. Set up inputs so each htseqcount run can be configured from the inputs.
- Created a miRNA pipeline
- Use name sorted bam for HTseq-count step