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example.json
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example.json
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{
"id": "APj3hc4v",
"dir": "projects/APj3hc4v",
"qc_dir": "projects/APj3hc4v/1_qc",
"raw_dir": "projects/APj3hc4v/0_raw_reads",
"align_dir": "projects/APj3hc4v/2_alignment",
"diff_dir": "projects/APj3hc4v/3_diff_exp",
"temp_dir": "projects/APj3hc4v/_temp",
"jobs": [
"ain68j",
"4ajwos",
"h07j25",
"fxkgre"
],
"raw_reads": {
"wt2": [
"0_raw_reads/wt2/18842_AGTTCC_L001_R1_002.fastq.gz",
"0_raw_reads/wt2/18842_AGTTCC_L002_R1_002.fastq.gz",
"0_raw_reads/wt2/18842_AGTTCC_L001_R1_003.fastq.gz",
"0_raw_reads/wt2/18842_AGTTCC_L001_R1_001.fastq.gz",
"0_raw_reads/wt2/18842_AGTTCC_L002_R1_001.fastq.gz",
"0_raw_reads/wt2/18842_AGTTCC_L002_R1_003.fastq.gz"
],
"mt3": [
"0_raw_reads/mt3/18846_GTGAAA_L001_R1_001.fastq.gz",
"0_raw_reads/mt3/18846_GTGAAA_L002_R1_003.fastq.gz",
"0_raw_reads/mt3/18846_GTGAAA_L001_R1_002.fastq.gz",
"0_raw_reads/mt3/18846_GTGAAA_L002_R1_001.fastq.gz",
"0_raw_reads/mt3/18846_GTGAAA_L002_R1_002.fastq.gz",
"0_raw_reads/mt3/18846_GTGAAA_L001_R1_003.fastq.gz"
],
"wt1": [
"0_raw_reads/wt1/18841_AGTCAA_L002_R1_003.fastq.gz",
"0_raw_reads/wt1/18841_AGTCAA_L001_R1_001.fastq.gz",
"0_raw_reads/wt1/18841_AGTCAA_L001_R1_003.fastq.gz",
"0_raw_reads/wt1/18841_AGTCAA_L002_R1_001.fastq.gz",
"0_raw_reads/wt1/18841_AGTCAA_L002_R1_002.fastq.gz",
"0_raw_reads/wt1/18841_AGTCAA_L001_R1_002.fastq.gz"
],
"mt2": [
"0_raw_reads/mt2/18845_GTCCGC_L002_R1_001.fastq.gz",
"0_raw_reads/mt2/18845_GTCCGC_L002_R1_002.fastq.gz",
"0_raw_reads/mt2/18845_GTCCGC_L001_R1_001.fastq.gz",
"0_raw_reads/mt2/18845_GTCCGC_L001_R1_003.fastq.gz",
"0_raw_reads/mt2/18845_GTCCGC_L002_R1_003.fastq.gz",
"0_raw_reads/mt2/18845_GTCCGC_L001_R1_002.fastq.gz"
],
"wt3": [
"0_raw_reads/wt3/18843_ATGTCA_L001_R1_002.fastq.gz",
"0_raw_reads/wt3/18843_ATGTCA_L002_R1_002.fastq.gz",
"0_raw_reads/wt3/18843_ATGTCA_L002_R1_001.fastq.gz",
"0_raw_reads/wt3/18843_ATGTCA_L002_R1_003.fastq.gz",
"0_raw_reads/wt3/18843_ATGTCA_L001_R1_003.fastq.gz",
"0_raw_reads/wt3/18843_ATGTCA_L001_R1_001.fastq.gz"
],
"mt1": [
"0_raw_reads/mt1/18844_CCGTCC_L002_R1_001.fastq.gz",
"0_raw_reads/mt1/18844_CCGTCC_L001_R1_002.fastq.gz",
"0_raw_reads/mt1/18844_CCGTCC_L002_R1_002.fastq.gz",
"0_raw_reads/mt1/18844_CCGTCC_L002_R1_003.fastq.gz",
"0_raw_reads/mt1/18844_CCGTCC_L001_R1_003.fastq.gz",
"0_raw_reads/mt1/18844_CCGTCC_L001_R1_001.fastq.gz"
]
},
"chk_md5": {},
"samples": {
"ASgyci7n": {
"id": "ASgyci7n",
"name": "wt2",
"type": 1,
"organism": "caenorhabditis_elegans",
"ref_ver": "235",
"length": 200,
"stdev": 60,
"bootstrap_n": 200,
"reads": [
"0_raw_reads/wt2/18842_AGTTCC_L001_R1_002.fastq.gz",
"0_raw_reads/wt2/18842_AGTTCC_L002_R1_002.fastq.gz",
"0_raw_reads/wt2/18842_AGTTCC_L001_R1_003.fastq.gz",
"0_raw_reads/wt2/18842_AGTTCC_L001_R1_001.fastq.gz",
"0_raw_reads/wt2/18842_AGTTCC_L002_R1_001.fastq.gz",
"0_raw_reads/wt2/18842_AGTTCC_L002_R1_003.fastq.gz"
],
"chk_md5": [],
"projects": [
"APj3hc4v"
],
"meta": {
"title": "sample_title",
"contributors": ["sample_contrib_one", "sample_contrib_two"],
"source": "sample_source",
"organism": "sample_organism",
"chars": {"genotype": "mt", "phenotype": "WBPhenotype:0001"},
"description": "sample_description",
"datetime": "2017-11-27 13:31:59"
}
},
"AShu0wib": {
"id": "AShu0wib",
"name": "mt3",
"type": 1,
"organism": "caenorhabditis_elegans",
"ref_ver": "235",
"length": 200,
"stdev": 60,
"bootstrap_n": 200,
"reads": [
"0_raw_reads/mt3/18846_GTGAAA_L001_R1_001.fastq.gz",
"0_raw_reads/mt3/18846_GTGAAA_L002_R1_003.fastq.gz",
"0_raw_reads/mt3/18846_GTGAAA_L001_R1_002.fastq.gz",
"0_raw_reads/mt3/18846_GTGAAA_L002_R1_001.fastq.gz",
"0_raw_reads/mt3/18846_GTGAAA_L002_R1_002.fastq.gz",
"0_raw_reads/mt3/18846_GTGAAA_L001_R1_003.fastq.gz"
],
"chk_md5": [],
"projects": [
"APj3hc4v"
],
"meta": {
"title": "",
"contributors": [],
"source": "",
"chars": {
"genotype": "mt"
},
"description": "",
"datetime": "2018-04-17 14:57:37"
}
},
"ASb8063z": {
"id": "ASb8063z",
"name": "wt1",
"type": 1,
"organism": "caenorhabditis_elegans",
"ref_ver": "235",
"length": 200,
"stdev": 60,
"bootstrap_n": 200,
"reads": [
"0_raw_reads/wt1/18841_AGTCAA_L002_R1_003.fastq.gz",
"0_raw_reads/wt1/18841_AGTCAA_L001_R1_001.fastq.gz",
"0_raw_reads/wt1/18841_AGTCAA_L001_R1_003.fastq.gz",
"0_raw_reads/wt1/18841_AGTCAA_L002_R1_001.fastq.gz",
"0_raw_reads/wt1/18841_AGTCAA_L002_R1_002.fastq.gz",
"0_raw_reads/wt1/18841_AGTCAA_L001_R1_002.fastq.gz"
],
"chk_md5": [],
"projects": [
"APj3hc4v"
],
"meta": {
"title": "",
"contributors": [],
"source": "",
"chars": {
"genotype": "wt"
},
"description": "",
"datetime": "2018-04-17 14:57:37"
}
},
"AStkqpz9": {
"id": "AStkqpz9",
"name": "mt2",
"type": 1,
"organism": "caenorhabditis_elegans",
"ref_ver": "235",
"length": 200,
"stdev": 60,
"bootstrap_n": 200,
"reads": [
"0_raw_reads/mt2/18845_GTCCGC_L002_R1_001.fastq.gz",
"0_raw_reads/mt2/18845_GTCCGC_L002_R1_002.fastq.gz",
"0_raw_reads/mt2/18845_GTCCGC_L001_R1_001.fastq.gz",
"0_raw_reads/mt2/18845_GTCCGC_L001_R1_003.fastq.gz",
"0_raw_reads/mt2/18845_GTCCGC_L002_R1_003.fastq.gz",
"0_raw_reads/mt2/18845_GTCCGC_L001_R1_002.fastq.gz"
],
"chk_md5": [],
"projects": [
"APj3hc4v"
],
"meta": {
"title": "",
"contributors": [],
"source": "",
"chars": {
"genotype": "mt"
},
"description": "",
"datetime": "2018-04-17 14:57:37"
}
},
"ASga23hd": {
"id": "ASga23hd",
"name": "wt3",
"type": 1,
"organism": "caenorhabditis_elegans",
"ref_ver": "235",
"length": 200,
"stdev": 60,
"bootstrap_n": 200,
"reads": [
"0_raw_reads/wt3/18843_ATGTCA_L001_R1_002.fastq.gz",
"0_raw_reads/wt3/18843_ATGTCA_L002_R1_002.fastq.gz",
"0_raw_reads/wt3/18843_ATGTCA_L002_R1_001.fastq.gz",
"0_raw_reads/wt3/18843_ATGTCA_L002_R1_003.fastq.gz",
"0_raw_reads/wt3/18843_ATGTCA_L001_R1_003.fastq.gz",
"0_raw_reads/wt3/18843_ATGTCA_L001_R1_001.fastq.gz"
],
"chk_md5": [],
"projects": [
"APj3hc4v"
],
"meta": {
"title": "",
"contributors": [],
"source": "",
"chars": {
"genotype": "wt"
},
"description": "",
"datetime": "2018-04-17 14:57:37"
}
},
"AS4bmpyw": {
"id": "AS4bmpyw",
"name": "mt1",
"type": 1,
"organism": "caenorhabditis_elegans",
"ref_ver": "235",
"length": 200,
"stdev": 60,
"bootstrap_n": 200,
"reads": [
"0_raw_reads/mt1/18844_CCGTCC_L002_R1_001.fastq.gz",
"0_raw_reads/mt1/18844_CCGTCC_L001_R1_002.fastq.gz",
"0_raw_reads/mt1/18844_CCGTCC_L002_R1_002.fastq.gz",
"0_raw_reads/mt1/18844_CCGTCC_L002_R1_003.fastq.gz",
"0_raw_reads/mt1/18844_CCGTCC_L001_R1_003.fastq.gz",
"0_raw_reads/mt1/18844_CCGTCC_L001_R1_001.fastq.gz"
],
"chk_md5": [],
"projects": [
"APj3hc4v"
],
"meta": {
"title": "",
"contributors": [],
"source": "",
"chars": {
"genotype": "mt"
},
"description": "",
"datetime": "2018-04-17 14:57:37"
}
}
},
"design": 1,
"ctrls": {
"ASgyci7n": "genotype",
"ASb8063z": "genotype",
"ASga23hd": "genotype"
},
"progress": 4,
"meta": {
"title": "Title",
"summary": "Summary",
"contributors": ["someone", "another"],
"SRA_center_code": "SRA CODE",
"email": "bob@example.com",
"datetime": "2017-11-27 13:31:24"
}
}