search

theislab / scib-pipeline

Snakemake pipeline that works with the scIB package to benchmark data integration methods.
MIT License
64 stars 28 forks source link

Lost Snakefile, snakefile, workflow/Snakefile, workflow/snakefile #58

Open Beki-seq opened 1 year ago

Beki-seq commented 1 year ago

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 commented 10 months ago

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).