snakemake profiles
linsalrob opened this issue · 2 comments
"Non-standard" default snakemake profiles are giving a hecatomb error.
I have followed Mike's snakemake profile tutorial, but then added things to both the sbatch command and the default-resources.
For example, our cluster has a partition setting (general vs GPU) with a default resource of general that has been missed by hecatomb.
We need to make sure that hecatomb is compatible with any profile, and I think we need to ensure we incorporate the users default-resources settings, and perhaps other settings too(?)
The launcher is reading the defaults for jobs, mem and time from the run config and passing it via the command line to snakemake under --default-resources. This overwrites any declarations for default resources in the profile. It's a little bit unnecessary anyway, so I've removed it and it should be fixed in the next release.
should be fixed in current version