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feat: add Snakemake profiles

BIOPZ-Bak Maciej requested to merge profiles into dev

Replace --cluster-config CL snakemake parameter with new a mechanism: profiles.

Snakemake profiles are, in structure, directories which encapsulate all the information required for snakemake call (all CL params as well as cluster-specific cluster configuration files, job submission and job status query wrappers).

More info:

Having a set of defined profiles snakemake call for zarp is reduced to (e.g.):

snakemake \
    --profile="../../profiles/slurm-conda" \

Notable mentions:

  • ${PWD} is not properly parsed from a profile YAML in one of the rules, we need to use relative paths within singularity-args: --bind arguments.
  • cleaned unnecessary mapping keywords between sbatch params in the snakemake CL params and the content of cluster configuration file; now the cluster config JSON is dedicated to slurm and thus contains exact specific slurm keywords.
  • Running the workflow on your own samples section in the README changed significantly since we now provide the profiles instead of the user having to create them on their own.


  • Wait for the last test of mine to finish: conda+slurm
  • Update manual test commands in the README
Edited by BIOPZ-Bak Maciej

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