{
    "WORKFLOWS": "FETCH,QC,TRIMMING,MAPPING,DE,DAS",
    "BINS": "",
    "MAXTHREADS": "10",
    "VERSION": "1.1.0",
    "SETTINGS": {
        "cystic_fibrosis_monsda": {
            "SAMPLES": [
                "SRR19451834",
                "SRR19451844",
                "SRR19451825",
                "SRR19451824",
                "SRR19451822",
                "SRR19451850",
                "SRR19451849",
                "SRR19451847",
                "SRR19451846",
                "SRR19451831"
            ],
            "SEQUENCING": "paired",
            "REFERENCE": "GENOMES/GRCh38.p13_clean.fa.gz",
            "ANNOTATION": {
                "GTF": "GENOMES/gencode.v37.annotation.gtf.gz",
                "GFF": ""
            },
            "GROUPS": [
                "female",
                "female",
                "female",
                "female",
                "female",
                "male",
                "male",
                "male",
                "male",
                "male"
            ],
            "TYPES": "",
            "BATCHES": "",
            "INDEX": "",
            "PREFIX": ""
        }
    },
    "FETCH": {
        "TOOLS": {
            "sra": "sra"
        },
        "cystic_fibrosis_monsda": {
            "sra": {
                "OPTIONS": {
                    "SRA": ""
                }
            }
        }
    },
    "QC": {
        "TOOLS": {
            "fastqc": "fastqc"
        },
        "cystic_fibrosis_monsda": {
            "fastqc": {
                "OPTIONS": {
                    "QC": "",
                    "MULTI": ""
                }
            }
        }
    },
    "TRIMMING": {
        "TOOLS": {
            "trimgalore": "trim_galore"
        },
        "cystic_fibrosis_monsda": {
            "trimgalore": {
                "OPTIONS": {
                    "TRIM": "-q 15 --length 8 -e 0.15"
                }
            }
        }
    },
    "MAPPING": {
        "TOOLS": {
            "star": "STAR"
        },
        "cystic_fibrosis_monsda": {
            "star": {
                "OPTIONS": {
                    "INDEX": "--sjdbGTFfeatureExon exon --sjdbGTFtagExonParentTranscript Parent --genomeSAindexNbases 13",
                    "MAP": "--sjdbGTFfeatureExon exon --sjdbGTFtagExonParentTranscript Parent --outSAMprimaryFlag AllBestScore",
                    "EXTENSION": ""
                }
            }
        }
    },
    "DE": {
        "TOOLS": {
            "deseq2": "Analysis/DE/DESEQ2.R",
            "edger": "Analysis/DE/EDGER.R"
        },
        "CUTOFFS": {
            "pvalue": "0.05",
            "lfc": "1.0"
        },
        "COMPARABLE": {
            "male-VS-female": [
                [
                    "male"
                ],
                [
                    "female"
                ]
            ]
        },
        "EXCLUDE": [],
        "cystic_fibrosis_monsda": {
            "deseq2": {
                "OPTIONS": {
                    "COUNT": "-t gene -g gene_id --fraction -O",
                    "DE": ""
                }
            },
            "edger": {
                "OPTIONS": {
                    "COUNT": "-t gene -g gene_id --fraction -O",
                    "DE": ""
                }
            }
        }
    },
    "DAS": {
        "TOOLS": {
            "diego": "Analysis/DAS/DIEGO.py",
            "edger": "Analysis/DAS/EDGER.R"
        },
        "CUTOFFS": {
            "pvalue": "0.05",
            "lfc": "1.0"
        },
        "COMPARABLE": {
            "male-VS-female": [
                [
                    "male"
                ],
                [
                    "female"
                ]
            ]
        },
        "EXCLUDE": [],
        "cystic_fibrosis_monsda": {
            "diego": {
                "OPTIONS": {
                    "COUNT": "-t exon -g gene_id -f --fraction -O",
                    "DAS": "-c 10 -d 3 -q 0.01 -z 1.0 -r"
                }
            },
            "edger": {
                "OPTIONS": {
                    "COUNT": "-t exon -g gene_id -f --fraction -O",
                    "DAS": ""
                }
            }
        }
    }
}