[Python] Snakemake access snakemake.config in profile config.yaml file

Discussão em 'Python' iniciado por Stack, Abril 2, 2025.

  1. Stack

    Stack Membro Participativo

    I want to run a pipeline on a cluster where the name of the jobs are of the form : smk-{config["simulation"]}-{rule}-{wildcards}. Can I just do :

    snakemake --profile slurm --configfile myconfig.yaml


    With slurm/config.yaml being :

    executor: slurm
    jobs: 64
    latency-wait: 30
    cluster:
    sbatch
    --partition=workq
    --job-name=smk-{config["simulation"]}-{rule}-{wildcards}
    [...]

    Continue reading...

Compartilhe esta Página