Missing Snakefile from example test dataset

[a-ludi]

Missing Snakefile from example test dataset

[a-ludi]

I suspect, that this might be because I am not using the correct Snakefile?

I agree. Try this Snakefile. It is the one that should be included in the tarball.

[davidjstudholme]

The link in your message above is: https://raw.githubusercontent.com/a-ludi/dentist/d85a86fda8da241b0de3d3b8d3b02cf9e3405302/snakemake/cluster.yml. This is file called 'cluster.yml' not 'Snakefile'. Is this intended?

[a-ludi]

This was a copy&paste mishap. Sorry. Correct link: https://raw.githubusercontent.com/a-ludi/dentist/d85a86fda8da241b0de3d3b8d3b02cf9e3405302/snakemake/Snakefile

[davidjstudholme]

Thanks, Arne.

However, with this file I now get this error message:

SyntaxError in line 896 of /home/djs217/dentist-example/Snakefile:
Unexpected keyword container in rule definition (Snakefile, line 896)

[davidjstudholme]

Possibly this is an issue with snakemake version used?

$ snakemake --version
5.10.0

[davidjstudholme]

The offending line 896 seems to be:

container: dentist_container

[a-ludi]

Possibly this is an issue with snakemake version used?
Yes, please update to v5.32.1.

[davidjstudholme]

Thanks, Arne. So, I think the original issue is now resolved since the the missing file is available at: https://raw.githubusercontent.com/a-ludi/dentist/d85a86fda8da241b0de3d3b8d3b02cf9e3405302/snakemake/Snakefile