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LepWrap is a wrapper for LepMap3 (Rastas 2017) and LepAnchor (Rastas 2020) intended to link the modules together into a single workflow. LepWrap does things a certain way, employing the most common/reasonable way of using Lep-Map3 (and LepAnchor, more or less). The current version is a lot more flexible than its predecessors, but might still lack something you're looking for. Your study is unique, and I encourage you to clone/fork this repository and adapt LepWrap to your needs! All of the code in LepWrap is written in human-readable bash or aggressively annotated R, so give it a shot and adapt it to your workflow. PR's welcome!
If using LepWrap and publishing, cite Pasi Rastas for his work on Lep-Map3 and Lep-Anchor, and if you like using it, star this repository and give me a shout out on Twitter @pvdimens 
Pasi Rastas, Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data, Bioinformatics, Volume 33, Issue 23, 01 December 2017, Pages 3726–3732,https://doi.org/10.1093/bioinformatics/btx494
Pasi Rastas, Lep-Anchor: automated construction of linkage map anchored haploid genomes, Bioinformatics, Volume 36, Issue 8, 15 April 2020, Pages 2359–2364, https://doi.org/10.1093/bioinformatics/btz978
Pavel V. Dimens. (2022). pdimens/LepWrap: link with zenodo (4.0). Zenodo. https://doi.org/10.5281/zenodo.6055565
