Data and ref2020 point outside the repo.

[reedacartwright]

Data and ref2020 are sybolic links that point to folders outside the repo. There are three solutions to fix this issue.

1. Add the data to the repository.
2. Post the data to FigShare or similar archival site and provide a script to download the data and setup the directory.
3. Include a readme describing how the data can be generated from your raw data.

[reedacartwright]

The input file for the mutation analysis will need similar archiving. It is 44.7 MB large.

[MaevaTecher]

Hi Reed,
Thanks for raising these issues.

For the data, we added the link to raw reads, input files for fastsimcoal2 are in the demography folder now. Since the vcf files are too heavy, I will upload them on a dryad repository, so if you can send me your input file as well via file sender I could upload altogether.

I added as much details as possible of the dependencies necessary, maybe for the Snakemake pipeline, I will export Sasha's condo environment for it. Please do not hesitate to modify the read me for the de novo mutation part.

If you have any additional suggestions, please do not hesitate.