BARM_tools/config.json at master · EnvGen/BARM_tools · GitHub

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{
    "global_tmp_dir": "$SNIC_TMP",
    "bowtie2_rules": {
        "load_env": "",
        "platform": "Illumina",
        "mapping_params": {
            "default": "",
            "local": "--local"
        }
    },
    "samtools_rules": {
        "load_env": "",
        "picard_jars": "/sw/apps/bioinfo/picard/1.118/milou",
        "threads_for_sorting": "16"
    },
    "bowtie2_quant_rules": {
        "load_env": "",
        "load_htseq_env": "",
        "gene_prediction": "prodigal",
        "references": {},
        "samples": {},
        "units": {},
        "reference_for_ref_set": {},
        "mapping_params": {
            "default": "",
            "local": "--local"
        },
        "prodigal_parameters_used": "default-meta",
        "mapper": "bowtie2",
        "scripts_dir": "scripts",
        "read_length_script": "toolbox/scripts/gene_length.py",
        "rpkm_table_script": "toolbox/scripts/rpkm_table.py",
        "tpm_table_script": "toolbox/scripts/tpm_table.py",
        "raw_counts_table_script": "toolbox/scripts/raw_counts.py",
        "split_ref_sets": {},
        "rpkm_annotations_table_script": "BLUEPRINT_pipeline/toolbox/scripts/rpkm_annotations_table.py"
    }
}