Lost Snakefile, snakefile, workflow/Snakefile, workflow/snakefile

[Beki-seq]

Hello,

Thank you for your pipeline.

The first question is that the paul15 file is not available from the link you provided.

The second question is, since I cannot find the paul15 file, I used my own dataset to run the code. When I run snakemake --configfile configs/test_data-R3.6.yaml, I encountered an error: "Error: no Snakefile found, tried Snakefile, snakefile, workflow/Snakefile, workflow/snakefile."

I am not sure where I went wrong. Could you please give me some hints? What I did was using scanpy to read all my objects and create an h5ad file. Then I ran the snakemake --configfile configs/test_data-R3.6.yaml command, making changes to the YAML file parameters based on my own requirements. That's when I got the error. I hope you could offer me some support with this.

Note: I corrected the typo "h3ad" to "h5ad" assuming it was a typographical error. If "h3ad" is indeed correct in your context, please ignore this correction.

[Simon-chevolleau]

Hello, I'm not related with Theis lab, but your error sounds like you ran the snakemake command elsewhere than the git repository (where the Snakefile file stands).