Initial release of nf-core/eager featuring:
- FastQC read quality control
- (Optional) Read complexity filtering with FastP
- Read merging and clipping using AdapterRemoval v2
- Mapping using BWA / BWA Mem or CircularMapper
- Library Complexity Estimation with Preseq
- Conversion and Filtering of BAM files using Samtools
- Damage assessment via DamageProfiler, additional filtering using PMDTools
- Duplication removal via DeDup
- BAM Clipping with BamUtil for UDGhalf protocols
- QualiMap BAM quality control analysis
Furthermore, this already creates an interactive report using MultiQC, which will be upgraded in V2.1 "Ulm" to contain more aDNA specific metrics.