{
        "project-name":"test-project",
        "outdir":"Results",
        "prinseq-meanquality":"30",
        "cutadapt-forward":"AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
        "cutadapt-reverse":"AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
        "library-type":"first-strand",
        "read-length":"100",
        "align-cpu":"1",
        "reference":
        {
                "name":"Ensembl_GRCh37",
                "description":"Homo sapiens Ensembl GRCh37",
                "STARindexDir":"CONFIG/genome",
                "fasta":"CONFIG/genome/human_g1k_v37.chr22.fasta",
                "gtf":"CONFIG/genome/chr22.gff",
                "biomart":"37,hsapiens_gene_ensembl"
        },
        "samplesCondition": [
                {
                        "name": "80_CT_1_chr22",
                        "condition": "CT"
                },
                {
                        "name": "81_CT_2_chr22",
                        "condition": "CT"
                },
                {
                        "name": "82_CT_3_chr22",
                        "condition": "CT"
                },
                {
                        "name": "83_CT_4_chr22",
                        "condition": "CT"
                },
                {
                        "name": "96_TREATED_1_chr22",
                        "condition": "TREATED"
                },
                {
                        "name": "97_TREATED_2_chr22",
                        "condition": "TREATED"
                },
                {
                        "name": "98_TREATED_3_chr22",
                        "condition": "TREATED"
                },
                {
                        "name": "99_TREATED_4_chr22",
                        "condition": "TREATED"
                }
        ],
        "comparisons": 
        {
                "TREATED__vs__CT": {
			"minLogFC": 0.58,
                        "condition1": "TREATED",
                        "condition2": "CT"
                }
        }
}