config.json-example

{
    "number_of_example_samples": 3,
    "number_of_files_per_sample": 2,
    "pipeline": "catsup-kraken2",
    "nextflow_additional_params": "-process.executor slurm",
    "container": "singularity",
    "pipelines":
    {
	"catsup-kraken2":
	{
	    "script": "/work/manual_runs/catsup/pipelines/catsup-kraken2/catsup-kraken2.nf",
	    "image": "/data/images/fatos-20200320T140813_2.2.img",
	    "human_ref": "/data/databases/clockworkcloud/kraken2/minikraken2_v2_8GB_201904_UPDATE"
	}

    },
    "upload":
    {
	"s3":
	{
	    "bucket": "s3://mmm-sp3-alpha",
	    "s3cmd-config": "/home/ubuntu/.s3cfg-catsup"
	}
    }
}