bwa_config.json

{
    "run_dir": "/bwa_pipeline",
    "data_dir": "/bwa_data",
    "result_dir": "/bwa_results",
    "tbprofiler_env": "TBprofiler2",
    "s3_conf": {
        "result_bucket_prefix": "bwa_mtb_result_"
    },
    "tools": {
	"snpeff": "java -Xmx8G -jar /snpEff/snpEff.jar",
	"snpsift": "java -Xmx8g -jar /snpEff/SnpSift.jar",
	"samtools": "samtools",
	"bwa": "bwa",
	"gatk": "gatk",
	"picard": "java -Xmx4g -jar /jarfiles/picard-2.27.5.jar",
	"varscan": "java -Xmx8g -jar /jarfiles/VarScan.v2.4.0.jar",
	"bcftools": "bcftools",
	"tabix": "tabix",
	"bgzip": "bgzip",
	"trim_galore": "trim_galore",
	"vceff_opl": "perl /snpEff/scripts/vcfEffOnePerLine.pl",
        "tbprofiler": "tb-profiler"
    },
    "fastq_patterns": ["*_{{readnum}}.fastq"],
    "tmp_dir": "/bwa_tmp",
    "organisms": {
	    "mmp": { "snpeff_db": "Methanococcus_maripaludis_s2" },
	    "dvh": { "snpeff_db": "Desulfovibrio_vulgaris_str_hildenborough" },
	    "hal": { "snpeff_db": "Halobacterium_salinarum_nrc_1" },
	    "msm": {
	        "snpeff_db": "Mycobacterium_smegmatis_str_mc2_155_gca_000767605",
	        "genome_gff": "GCF_000767605.1_ASM767605v1_genomic.gff",
	        "genome_fasta": "GCF_000767605.1_ASM76760v1_genomic.fna"
	    },
	    "mtb": {
	        "snpeff_db": "Mycobacterium_tuberculosis_h37rv",
	        "genome_gff": "GCF_000195955.2_ASM19595v2_genomic_modified.gff",
	        "genome_fasta": "GCF_000195955.2_ASM19595v2_genomic_modified.fna"
	    }
    }
}