pipelines.chromake.scripts.config.update_jobs

pipelines.chromake.scripts.config.update_jobs(config_path, jobs)

Update or add the JOBS section in an existing YAML config.

CORES_PER_JOBS: number of cpu cores to use for each jobs (>=1)

QOS_INFOS: if using an executor like slurm, indicate the name of the qos (e.g. short), and the associated MaxWall in minutes.

Parameters

Name	Type	Description	Default
config_path	str	Path to the YAML config file.	required
jobs	dict	Dictionary containing JOBS information to update. Can be a full replacement or partial update.	required

Example

jobs_update = {
    "CORES_PER_JOBS": {
        "FASTQC": 10,
        "CUTADAPT": 10,
        "BOWTIE2": 30,
        "SAMTOOLS_QC": 5,
        "MULTIBAMSUMMARY": 5,
        "BEDTOOLS": 5
    },
    "QOS_INFOS": {
        "short": {"MaxWall": 2000},
        "medium": {"MaxWall": 5000},
        "long": {"MaxWall": 15000} 
    }
}
update_jobs("config.yaml", jobs_update)