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shandley / hecatomb

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
MIT License
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snakemake profiles #56

Closed linsalrob closed 2 years ago

linsalrob commented 2 years ago

"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(?)

beardymcjohnface commented 2 years ago

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.

beardymcjohnface commented 2 years ago

should be fixed in current version