@guillermoNR Ah, ok, that’s a lot of helpful information to understand what you’re doing. Thanks!
You’ll need all (or mostly all) of the files in the https://github.com/nextstrain/dengue repository. That you downloaded just a few of the files is the reason why you see the “Missing input files” errors in your second screenshot.
Probably the easiest way to download the whole repository is by navigating to https://github.com/nextstrain/dengue, clicking the green “Code” button, and clicking “Download ZIP”. This is a snapshot of the repository at the time of download. Extracting the ZIP file produces a dengue-main folder on your computer.
You can also download the repository using the git command, if you have that, with:
git clone https://github.com/nextstrain/dengue
This downloads the entire history of the repository, and it would be possible for you in the future to fetch updates we make to the repository using other git commands. This produces a dengue folder on your computer.
Once you have a folder with a complete copy of the repository, you can verify it works for you and then start making modifications if you need any.
Regarding your screenshot of the unintelligible metadata_all.tsv.zst file you downloaded, that looks to me like the file was not uncompressed with unzstd first. Notepad is attempting to show as text data that’s not text. You can either manually decompress the file to turn the compressed metadata_all.tsv.zst into a plain text metadata_all.tsv, or let the Snakemake workflow do that and find the uncompressed copies in results/.
I’ll also tag in @quietjen as she’s been working on our dengue workflow recently and may be able to offer more help.