Hi,
I'm wondering if you'd be able to help me understand how to construct a correct JSON config file. My goal is to demultiplex based on 6bp I1 indices from 4 files provided by our sequencing center (we have I2, but it's meaningless in this case).
What I've tried:
- Constructing a json file based on the templates you had in the documentation, and then running it through the python script you provided:
pheniqs/tool/pheniqs-io-api.py -c 211123_run064_pheniqs_test.json -LS -F fastq --compression gz > 211129_run064_pheniqs_post-io-api.json.
Where I'm confused
When I try to run pheniqs as follows pheniqs mux -F fastq --compression gz -c 211129_run064_pheniqs_post-io-api.json, it just prints the gzip-compressed output to standard out. Yet in the config JSON produced using your python script there are filenames as output. When I run the validate step, it also specifies output will be put to stdout which is a bit confusing to me. I've provided both configs in plaintext below.
Please accept my apologies for the vague query, but I am a bit stumped. I'm unfamiliar with JSON-formatted configs and used to providing this info in a TSV/CSV and am not quite sure where to start in troubleshooting this. Even if you can tell me this must be due to some stray punctuation / a missing section in my original config or some such issue that would be really helpful for me to understand how pheniqs works.
Thanks a lot for your help,
Jesse
Original JSON file I constructed with your template:
{
"PL" : "ILLUMINA",
"PM" : "NovaSeq_2x250_UCDavis_run064",
"base input url": ".",
"filter incoming qc fail" : true,
"flowcell id" : "JMSNRSCF",
"report url" : "211123_JMSNRSCF_demux_sample_report.json",
"input" : [
"JMSNRSCF_S1_L001_R1_001.fastq.gz",
"JMSNRSCF_S1_L001_I1_001.fastq.gz",
"JMSNRSCF_S1_L001_I2_001.fastq.gz",
"JMSNRSCF_S1_L001_R2_001.fastq.gz"
],
"template" : {
"transform" : {
"token" : [ "0::", "3::" ]
}
},
"sample" : {
"transform" : {
"token" : [ "1::6" ]
},
"algorithm" : "pamld",
"confidence threshold" : 0.95,
"noise" : 0.05,
"codec" : {
"@11_15": {
"LB": "11_15",
"barcode": [
"AGTCAA"
],
"output": [
"JMSNRSCF_11_15_s01.fastq.gz",
"JMSNRSCF_11_15_s02.fastq.gz",
"JMSNRSCF_11_15_s03.fastq.gz",
"JMSNRSCF_11_15_s04.fastq.gz"
]
},
"@11_200": {
"LB": "11_200",
"barcode": [
"ATGTCA"
],
"output": [
"JMSNRSCF_11_200_s01.fastq.gz",
"JMSNRSCF_11_200_s02.fastq.gz",
"JMSNRSCF_11_200_s03.fastq.gz",
"JMSNRSCF_11_200_s04.fastq.gz"
]
},
"@11_25": {
"LB": "11_25",
"barcode": [
"CGTACG"
],
"output": [
"JMSNRSCF_11_25_s01.fastq.gz",
"JMSNRSCF_11_25_s02.fastq.gz",
"JMSNRSCF_11_25_s03.fastq.gz",
"JMSNRSCF_11_25_s04.fastq.gz"
]
},
"@2_120": {
"LB": "2_120",
"barcode": [
"AGTCAA"
],
"output": [
"JMSNRSCF_2_120_s01.fastq.gz",
"JMSNRSCF_2_120_s02.fastq.gz",
"JMSNRSCF_2_120_s03.fastq.gz",
"JMSNRSCF_2_120_s04.fastq.gz"
]
},
"@2_400": {
"LB": "2_400",
"barcode": [
"ATCTCA"
],
"output": [
"JMSNRSCF_2_400_s01.fastq.gz",
"JMSNRSCF_2_400_s02.fastq.gz",
"JMSNRSCF_2_400_s03.fastq.gz",
"JMSNRSCF_2_400_s04.fastq.gz"
]
},
"@2_45": {
"LB": "2_45",
"barcode": [
"AGGAAT"
],
"output": [
"JMSNRSCF_2_45_s01.fastq.gz",
"JMSNRSCF_2_45_s02.fastq.gz",
"JMSNRSCF_2_45_s03.fastq.gz",
"JMSNRSCF_2_45_s04.fastq.gz"
]
},
"@7_120": {
"LB": "7_120",
"barcode": [
"ATTCCT"
],
"output": [
"JMSNRSCF_7_120_s01.fastq.gz",
"JMSNRSCF_7_120_s02.fastq.gz",
"JMSNRSCF_7_120_s03.fastq.gz",
"JMSNRSCF_7_120_s04.fastq.gz"
]
},
"@7_200": {
"LB": "7_200",
"barcode": [
"GTGGCC"
],
"output": [
"JMSNRSCF_7_200_s01.fastq.gz",
"JMSNRSCF_7_200_s02.fastq.gz",
"JMSNRSCF_7_200_s03.fastq.gz",
"JMSNRSCF_7_200_s04.fastq.gz"
]
},
"@7_25": {
"LB": "7_25",
"barcode": [
"GTGAAA"
],
"output": [
"JMSNRSCF_7_25_s01.fastq.gz",
"JMSNRSCF_7_25_s02.fastq.gz",
"JMSNRSCF_7_25_s03.fastq.gz",
"JMSNRSCF_7_25_s04.fastq.gz"
]
},
"@7_45": {
"LB": "7_45",
"barcode": [
"ATGAGC"
],
"output": [
"JMSNRSCF_7_45_s01.fastq.gz",
"JMSNRSCF_7_45_s02.fastq.gz",
"JMSNRSCF_7_45_s03.fastq.gz",
"JMSNRSCF_7_45_s04.fastq.gz"
]
},
"@8_200": {
"LB": "8_200",
"barcode": [
"ATGAGC"
],
"output": [
"JMSNRSCF_8_200_s01.fastq.gz",
"JMSNRSCF_8_200_s02.fastq.gz",
"JMSNRSCF_8_200_s03.fastq.gz",
"JMSNRSCF_8_200_s04.fastq.gz"
]
},
"@8_800": {
"LB": "8_800",
"barcode": [
"CCGTCC"
],
"output": [
"JMSNRSCF_8_800_s01.fastq.gz",
"JMSNRSCF_8_800_s02.fastq.gz",
"JMSNRSCF_8_800_s03.fastq.gz",
"JMSNRSCF_8_800_s04.fastq.gz"
]
},
"@9_200": {
"LB": "9_200",
"barcode": [
"ACTTCC"
],
"output": [
"JMSNRSCF_9_200_s01.fastq.gz",
"JMSNRSCF_9_200_s02.fastq.gz",
"JMSNRSCF_9_200_s03.fastq.gz",
"JMSNRSCF_9_200_s04.fastq.gz"
]
},
"@BGT_PL01_rev11": {
"LB": "BGT_PL01_rev11",
"barcode": [
"GCGGAC"
],
"output": [
"JMSNRSCF_BGT_PL01_rev11_s01.fastq.gz",
"JMSNRSCF_BGT_PL01_rev11_s02.fastq.gz",
"JMSNRSCF_BGT_PL01_rev11_s03.fastq.gz",
"JMSNRSCF_BGT_PL01_rev11_s04.fastq.gz"
]
},
"@BGT_PL01_rev12": {
"LB": "BGT_PL01_rev12",
"barcode": [
"TTTCAC"
],
"output": [
"JMSNRSCF_BGT_PL01_rev12_s01.fastq.gz",
"JMSNRSCF_BGT_PL01_rev12_s02.fastq.gz",
"JMSNRSCF_BGT_PL01_rev12_s03.fastq.gz",
"JMSNRSCF_BGT_PL01_rev12_s04.fastq.gz"
]
},
"@BGT_PL01_rev13": {
"LB": "BGT_PL01_rev13",
"barcode": [
"CCGGTG"
],
"output": [
"JMSNRSCF_BGT_PL01_rev13_s01.fastq.gz",
"JMSNRSCF_BGT_PL01_rev13_s02.fastq.gz",
"JMSNRSCF_BGT_PL01_rev13_s03.fastq.gz",
"JMSNRSCF_BGT_PL01_rev13_s04.fastq.gz"
]
},
"@BGT_PL01_rev14": {
"LB": "BGT_PL01_rev14",
"barcode": [
"ATCGTG"
],
"output": [
"JMSNRSCF_BGT_PL01_rev14_s01.fastq.gz",
"JMSNRSCF_BGT_PL01_rev14_s02.fastq.gz",
"JMSNRSCF_BGT_PL01_rev14_s03.fastq.gz",
"JMSNRSCF_BGT_PL01_rev14_s04.fastq.gz"
]
},
"@BGT_PL02_rev15": {
"LB": "BGT_PL02_rev15",
"barcode": [
"TGAGTG"
],
"output": [
"JMSNRSCF_BGT_PL02_rev15_s01.fastq.gz",
"JMSNRSCF_BGT_PL02_rev15_s02.fastq.gz",
"JMSNRSCF_BGT_PL02_rev15_s03.fastq.gz",
"JMSNRSCF_BGT_PL02_rev15_s04.fastq.gz"
]
},
"@BGT_PL02_rev16": {
"LB": "BGT_PL02_rev16",
"barcode": [
"CGCCTG"
],
"output": [
"JMSNRSCF_BGT_PL02_rev16_s01.fastq.gz",
"JMSNRSCF_BGT_PL02_rev16_s02.fastq.gz",
"JMSNRSCF_BGT_PL02_rev16_s03.fastq.gz",
"JMSNRSCF_BGT_PL02_rev16_s04.fastq.gz"
]
},
"@CAP_PL01_rev01": {
"LB": "CAP_PL01_rev01",
"barcode": [
"CGTGAT"
],
"output": [
"JMSNRSCF_CAP_PL01_rev01_s01.fastq.gz",
"JMSNRSCF_CAP_PL01_rev01_s02.fastq.gz",
"JMSNRSCF_CAP_PL01_rev01_s03.fastq.gz",
"JMSNRSCF_CAP_PL01_rev01_s04.fastq.gz"
]
},
"@CAP_PL01_rev02": {
"LB": "CAP_PL01_rev02",
"barcode": [
"ACATCG"
],
"output": [
"JMSNRSCF_CAP_PL01_rev02_s01.fastq.gz",
"JMSNRSCF_CAP_PL01_rev02_s02.fastq.gz",
"JMSNRSCF_CAP_PL01_rev02_s03.fastq.gz",
"JMSNRSCF_CAP_PL01_rev02_s04.fastq.gz"
]
},
"@CAP_PL01_rev03": {
"LB": "CAP_PL01_rev03",
"barcode": [
"GCCTAA"
],
"output": [
"JMSNRSCF_CAP_PL01_rev03_s01.fastq.gz",
"JMSNRSCF_CAP_PL01_rev03_s02.fastq.gz",
"JMSNRSCF_CAP_PL01_rev03_s03.fastq.gz",
"JMSNRSCF_CAP_PL01_rev03_s04.fastq.gz"
]
},
"@CAP_PL01_rev04": {
"LB": "CAP_PL01_rev04",
"barcode": [
"TGGTCA"
],
"output": [
"JMSNRSCF_CAP_PL01_rev04_s01.fastq.gz",
"JMSNRSCF_CAP_PL01_rev04_s02.fastq.gz",
"JMSNRSCF_CAP_PL01_rev04_s03.fastq.gz",
"JMSNRSCF_CAP_PL01_rev04_s04.fastq.gz"
]
},
"@Colette_rev21": {
"LB": "Colette_rev21",
"barcode": [
"TTCGTC"
],
"output": [
"JMSNRSCF_Colette_rev21_s01.fastq.gz",
"JMSNRSCF_Colette_rev21_s02.fastq.gz",
"JMSNRSCF_Colette_rev21_s03.fastq.gz",
"JMSNRSCF_Colette_rev21_s04.fastq.gz"
]
},
"@Colette_rev22": {
"LB": "Colette_rev22",
"barcode": [
"CCAACT"
],
"output": [
"JMSNRSCF_Colette_rev22_s01.fastq.gz",
"JMSNRSCF_Colette_rev22_s02.fastq.gz",
"JMSNRSCF_Colette_rev22_s03.fastq.gz",
"JMSNRSCF_Colette_rev22_s04.fastq.gz"
]
},
"@Colette_rev23": {
"LB": "Colette_rev23",
"barcode": [
"TCAGTT"
],
"output": [
"JMSNRSCF_Colette_rev23_s01.fastq.gz",
"JMSNRSCF_Colette_rev23_s02.fastq.gz",
"JMSNRSCF_Colette_rev23_s03.fastq.gz",
"JMSNRSCF_Colette_rev23_s04.fastq.gz"
]
},
"@Colette_rev24": {
"LB": "Colette_rev24",
"barcode": [
"CTGACC"
],
"output": [
"JMSNRSCF_Colette_rev24_s01.fastq.gz",
"JMSNRSCF_Colette_rev24_s02.fastq.gz",
"JMSNRSCF_Colette_rev24_s03.fastq.gz",
"JMSNRSCF_Colette_rev24_s04.fastq.gz"
]
},
"@Delaney_rev19": {
"LB": "Delaney_rev19",
"barcode": [
"GGAACT"
],
"output": [
"JMSNRSCF_Delaney_rev19_s01.fastq.gz",
"JMSNRSCF_Delaney_rev19_s02.fastq.gz",
"JMSNRSCF_Delaney_rev19_s03.fastq.gz",
"JMSNRSCF_Delaney_rev19_s04.fastq.gz"
]
},
"@Delaney_rev20": {
"LB": "Delaney_rev20",
"barcode": [
"CGAAAC"
],
"output": [
"JMSNRSCF_Delaney_rev20_s01.fastq.gz",
"JMSNRSCF_Delaney_rev20_s02.fastq.gz",
"JMSNRSCF_Delaney_rev20_s03.fastq.gz",
"JMSNRSCF_Delaney_rev20_s04.fastq.gz"
]
},
"@Rae_rev05": {
"LB": "Rae_rev05",
"barcode": [
"CACTGT"
],
"output": [
"JMSNRSCF_Rae_rev05_s01.fastq.gz",
"JMSNRSCF_Rae_rev05_s02.fastq.gz",
"JMSNRSCF_Rae_rev05_s03.fastq.gz",
"JMSNRSCF_Rae_rev05_s04.fastq.gz"
]
},
"@mystery12264": {
"LB": "mystery12264",
"barcode": [
"ACTGAT"
],
"output": [
"JMSNRSCF_mystery12264_s01.fastq.gz",
"JMSNRSCF_mystery12264_s02.fastq.gz",
"JMSNRSCF_mystery12264_s03.fastq.gz",
"JMSNRSCF_mystery12264_s04.fastq.gz"
]
},
"@mystery17075": {
"LB": "mystery17075",
"barcode": [
"GTGGCC"
],
"output": [
"JMSNRSCF_mystery17075_s01.fastq.gz",
"JMSNRSCF_mystery17075_s02.fastq.gz",
"JMSNRSCF_mystery17075_s03.fastq.gz",
"JMSNRSCF_mystery17075_s04.fastq.gz"
]
},
"@mystery4368": {
"LB": "mystery4368",
"barcode": [
"CGCCTG"
],
"output": [
"JMSNRSCF_mystery4368_s01.fastq.gz",
"JMSNRSCF_mystery4368_s02.fastq.gz",
"JMSNRSCF_mystery4368_s03.fastq.gz",
"JMSNRSCF_mystery4368_s04.fastq.gz"
]
},
"@mystery4895": {
"LB": "mystery4895",
"barcode": [
"GGGGGG"
],
"output": [
"JMSNRSCF_mystery4895_s01.fastq.gz",
"JMSNRSCF_mystery4895_s02.fastq.gz",
"JMSNRSCF_mystery4895_s03.fastq.gz",
"JMSNRSCF_mystery4895_s04.fastq.gz"
]
},
"@mystery8619": {
"LB": "mystery8619",
"barcode": [
"AGTTCC"
],
"output": [
"JMSNRSCF_mystery8619_s01.fastq.gz",
"JMSNRSCF_mystery8619_s02.fastq.gz",
"JMSNRSCF_mystery8619_s03.fastq.gz",
"JMSNRSCF_mystery8619_s04.fastq.gz"
]
},
"@mystery9788": {
"LB": "mystery9788",
"barcode": [
"CCGTCC"
],
"output": [
"JMSNRSCF_mystery9788_s01.fastq.gz",
"JMSNRSCF_mystery9788_s02.fastq.gz",
"JMSNRSCF_mystery9788_s03.fastq.gz",
"JMSNRSCF_mystery9788_s04.fastq.gz"
]
}
}
}
}
The output of your python processing script:
{
"PL": "ILLUMINA",
"PM": "NovaSeq_2x250_UCDavis_run064",
"base input url": ".",
"filter incoming qc fail": true,
"flowcell id": "JMSNRSCF",
"input": [
"JMSNRSCF_S1_L001_R1_001.fastq.gz",
"JMSNRSCF_S1_L001_I1_001.fastq.gz",
"JMSNRSCF_S1_L001_I2_001.fastq.gz",
"JMSNRSCF_S1_L001_R2_001.fastq.gz"
],
"report url": "211123_JMSNRSCF_demux_sample_report.json",
"sample": {
"algorithm": "pamld",
"codec": {
"@11_15": {
"LB": "11_15",
"barcode": [
"AGTCAA"
],
"output": [
"JMSNRSCF_11_15_s01.fastq.gz",
"JMSNRSCF_11_15_s02.fastq.gz",
"JMSNRSCF_11_15_s03.fastq.gz",
"JMSNRSCF_11_15_s04.fastq.gz"
]
},
"@11_200": {
"LB": "11_200",
"barcode": [
"ATGTCA"
],
"output": [
"JMSNRSCF_11_200_s01.fastq.gz",
"JMSNRSCF_11_200_s02.fastq.gz",
"JMSNRSCF_11_200_s03.fastq.gz",
"JMSNRSCF_11_200_s04.fastq.gz"
]
},
"@11_25": {
"LB": "11_25",
"barcode": [
"CGTACG"
],
"output": [
"JMSNRSCF_11_25_s01.fastq.gz",
"JMSNRSCF_11_25_s02.fastq.gz",
"JMSNRSCF_11_25_s03.fastq.gz",
"JMSNRSCF_11_25_s04.fastq.gz"
]
},
"@2_120": {
"LB": "2_120",
"barcode": [
"AGTCAA"
],
"output": [
"JMSNRSCF_2_120_s01.fastq.gz",
"JMSNRSCF_2_120_s02.fastq.gz",
"JMSNRSCF_2_120_s03.fastq.gz",
"JMSNRSCF_2_120_s04.fastq.gz"
]
},
"@2_400": {
"LB": "2_400",
"barcode": [
"ATCTCA"
],
"output": [
"JMSNRSCF_2_400_s01.fastq.gz",
"JMSNRSCF_2_400_s02.fastq.gz",
"JMSNRSCF_2_400_s03.fastq.gz",
"JMSNRSCF_2_400_s04.fastq.gz"
]
},
"@2_45": {
"LB": "2_45",
"barcode": [
"AGGAAT"
],
"output": [
"JMSNRSCF_2_45_s01.fastq.gz",
"JMSNRSCF_2_45_s02.fastq.gz",
"JMSNRSCF_2_45_s03.fastq.gz",
"JMSNRSCF_2_45_s04.fastq.gz"
]
},
"@7_120": {
"LB": "7_120",
"barcode": [
"ATTCCT"
],
"output": [
"JMSNRSCF_7_120_s01.fastq.gz",
"JMSNRSCF_7_120_s02.fastq.gz",
"JMSNRSCF_7_120_s03.fastq.gz",
"JMSNRSCF_7_120_s04.fastq.gz"
]
},
"@7_200": {
"LB": "7_200",
"barcode": [
"GTGGCC"
],
"output": [
"JMSNRSCF_7_200_s01.fastq.gz",
"JMSNRSCF_7_200_s02.fastq.gz",
"JMSNRSCF_7_200_s03.fastq.gz",
"JMSNRSCF_7_200_s04.fastq.gz"
]
},
"@7_25": {
"LB": "7_25",
"barcode": [
"GTGAAA"
],
"output": [
"JMSNRSCF_7_25_s01.fastq.gz",
"JMSNRSCF_7_25_s02.fastq.gz",
"JMSNRSCF_7_25_s03.fastq.gz",
"JMSNRSCF_7_25_s04.fastq.gz"
]
},
"@7_45": {
"LB": "7_45",
"barcode": [
"ATGAGC"
],
"output": [
"JMSNRSCF_7_45_s01.fastq.gz",
"JMSNRSCF_7_45_s02.fastq.gz",
"JMSNRSCF_7_45_s03.fastq.gz",
"JMSNRSCF_7_45_s04.fastq.gz"
]
},
"@8_200": {
"LB": "8_200",
"barcode": [
"ATGAGC"
],
"output": [
"JMSNRSCF_8_200_s01.fastq.gz",
"JMSNRSCF_8_200_s02.fastq.gz",
"JMSNRSCF_8_200_s03.fastq.gz",
"JMSNRSCF_8_200_s04.fastq.gz"
]
},
"@8_800": {
"LB": "8_800",
"barcode": [
"CCGTCC"
],
"output": [
"JMSNRSCF_8_800_s01.fastq.gz",
"JMSNRSCF_8_800_s02.fastq.gz",
"JMSNRSCF_8_800_s03.fastq.gz",
"JMSNRSCF_8_800_s04.fastq.gz"
]
},
"@9_200": {
"LB": "9_200",
"barcode": [
"ACTTCC"
],
"output": [
"JMSNRSCF_9_200_s01.fastq.gz",
"JMSNRSCF_9_200_s02.fastq.gz",
"JMSNRSCF_9_200_s03.fastq.gz",
"JMSNRSCF_9_200_s04.fastq.gz"
]
},
"@BGT_PL01_rev11": {
"LB": "BGT_PL01_rev11",
"barcode": [
"GCGGAC"
],
"output": [
"JMSNRSCF_BGT_PL01_rev11_s01.fastq.gz",
"JMSNRSCF_BGT_PL01_rev11_s02.fastq.gz",
"JMSNRSCF_BGT_PL01_rev11_s03.fastq.gz",
"JMSNRSCF_BGT_PL01_rev11_s04.fastq.gz"
]
},
"@BGT_PL01_rev12": {
"LB": "BGT_PL01_rev12",
"barcode": [
"TTTCAC"
],
"output": [
"JMSNRSCF_BGT_PL01_rev12_s01.fastq.gz",
"JMSNRSCF_BGT_PL01_rev12_s02.fastq.gz",
"JMSNRSCF_BGT_PL01_rev12_s03.fastq.gz",
"JMSNRSCF_BGT_PL01_rev12_s04.fastq.gz"
]
},
"@BGT_PL01_rev13": {
"LB": "BGT_PL01_rev13",
"barcode": [
"CCGGTG"
],
"output": [
"JMSNRSCF_BGT_PL01_rev13_s01.fastq.gz",
"JMSNRSCF_BGT_PL01_rev13_s02.fastq.gz",
"JMSNRSCF_BGT_PL01_rev13_s03.fastq.gz",
"JMSNRSCF_BGT_PL01_rev13_s04.fastq.gz"
]
},
"@BGT_PL01_rev14": {
"LB": "BGT_PL01_rev14",
"barcode": [
"ATCGTG"
],
"output": [
"JMSNRSCF_BGT_PL01_rev14_s01.fastq.gz",
"JMSNRSCF_BGT_PL01_rev14_s02.fastq.gz",
"JMSNRSCF_BGT_PL01_rev14_s03.fastq.gz",
"JMSNRSCF_BGT_PL01_rev14_s04.fastq.gz"
]
},
"@BGT_PL02_rev15": {
"LB": "BGT_PL02_rev15",
"barcode": [
"TGAGTG"
],
"output": [
"JMSNRSCF_BGT_PL02_rev15_s01.fastq.gz",
"JMSNRSCF_BGT_PL02_rev15_s02.fastq.gz",
"JMSNRSCF_BGT_PL02_rev15_s03.fastq.gz",
"JMSNRSCF_BGT_PL02_rev15_s04.fastq.gz"
]
},
"@BGT_PL02_rev16": {
"LB": "BGT_PL02_rev16",
"barcode": [
"CGCCTG"
],
"output": [
"JMSNRSCF_BGT_PL02_rev16_s01.fastq.gz",
"JMSNRSCF_BGT_PL02_rev16_s02.fastq.gz",
"JMSNRSCF_BGT_PL02_rev16_s03.fastq.gz",
"JMSNRSCF_BGT_PL02_rev16_s04.fastq.gz"
]
},
"@CAP_PL01_rev01": {
"LB": "CAP_PL01_rev01",
"barcode": [
"CGTGAT"
],
"output": [
"JMSNRSCF_CAP_PL01_rev01_s01.fastq.gz",
"JMSNRSCF_CAP_PL01_rev01_s02.fastq.gz",
"JMSNRSCF_CAP_PL01_rev01_s03.fastq.gz",
"JMSNRSCF_CAP_PL01_rev01_s04.fastq.gz"
]
},
"@CAP_PL01_rev02": {
"LB": "CAP_PL01_rev02",
"barcode": [
"ACATCG"
],
"output": [
"JMSNRSCF_CAP_PL01_rev02_s01.fastq.gz",
"JMSNRSCF_CAP_PL01_rev02_s02.fastq.gz",
"JMSNRSCF_CAP_PL01_rev02_s03.fastq.gz",
"JMSNRSCF_CAP_PL01_rev02_s04.fastq.gz"
]
},
"@CAP_PL01_rev03": {
"LB": "CAP_PL01_rev03",
"barcode": [
"GCCTAA"
],
"output": [
"JMSNRSCF_CAP_PL01_rev03_s01.fastq.gz",
"JMSNRSCF_CAP_PL01_rev03_s02.fastq.gz",
"JMSNRSCF_CAP_PL01_rev03_s03.fastq.gz",
"JMSNRSCF_CAP_PL01_rev03_s04.fastq.gz"
]
},
"@CAP_PL01_rev04": {
"LB": "CAP_PL01_rev04",
"barcode": [
"TGGTCA"
],
"output": [
"JMSNRSCF_CAP_PL01_rev04_s01.fastq.gz",
"JMSNRSCF_CAP_PL01_rev04_s02.fastq.gz",
"JMSNRSCF_CAP_PL01_rev04_s03.fastq.gz",
"JMSNRSCF_CAP_PL01_rev04_s04.fastq.gz"
]
},
"@Colette_rev21": {
"LB": "Colette_rev21",
"barcode": [
"TTCGTC"
],
"output": [
"JMSNRSCF_Colette_rev21_s01.fastq.gz",
"JMSNRSCF_Colette_rev21_s02.fastq.gz",
"JMSNRSCF_Colette_rev21_s03.fastq.gz",
"JMSNRSCF_Colette_rev21_s04.fastq.gz"
]
},
"@Colette_rev22": {
"LB": "Colette_rev22",
"barcode": [
"CCAACT"
],
"output": [
"JMSNRSCF_Colette_rev22_s01.fastq.gz",
"JMSNRSCF_Colette_rev22_s02.fastq.gz",
"JMSNRSCF_Colette_rev22_s03.fastq.gz",
"JMSNRSCF_Colette_rev22_s04.fastq.gz"
]
},
"@Colette_rev23": {
"LB": "Colette_rev23",
"barcode": [
"TCAGTT"
],
"output": [
"JMSNRSCF_Colette_rev23_s01.fastq.gz",
"JMSNRSCF_Colette_rev23_s02.fastq.gz",
"JMSNRSCF_Colette_rev23_s03.fastq.gz",
"JMSNRSCF_Colette_rev23_s04.fastq.gz"
]
},
"@Colette_rev24": {
"LB": "Colette_rev24",
"barcode": [
"CTGACC"
],
"output": [
"JMSNRSCF_Colette_rev24_s01.fastq.gz",
"JMSNRSCF_Colette_rev24_s02.fastq.gz",
"JMSNRSCF_Colette_rev24_s03.fastq.gz",
"JMSNRSCF_Colette_rev24_s04.fastq.gz"
]
},
"@Delaney_rev19": {
"LB": "Delaney_rev19",
"barcode": [
"GGAACT"
],
"output": [
"JMSNRSCF_Delaney_rev19_s01.fastq.gz",
"JMSNRSCF_Delaney_rev19_s02.fastq.gz",
"JMSNRSCF_Delaney_rev19_s03.fastq.gz",
"JMSNRSCF_Delaney_rev19_s04.fastq.gz"
]
},
"@Delaney_rev20": {
"LB": "Delaney_rev20",
"barcode": [
"CGAAAC"
],
"output": [
"JMSNRSCF_Delaney_rev20_s01.fastq.gz",
"JMSNRSCF_Delaney_rev20_s02.fastq.gz",
"JMSNRSCF_Delaney_rev20_s03.fastq.gz",
"JMSNRSCF_Delaney_rev20_s04.fastq.gz"
]
},
"@Rae_rev05": {
"LB": "Rae_rev05",
"barcode": [
"CACTGT"
],
"output": [
"JMSNRSCF_Rae_rev05_s01.fastq.gz",
"JMSNRSCF_Rae_rev05_s02.fastq.gz",
"JMSNRSCF_Rae_rev05_s03.fastq.gz",
"JMSNRSCF_Rae_rev05_s04.fastq.gz"
]
},
"@mystery12264": {
"LB": "mystery12264",
"barcode": [
"ACTGAT"
],
"output": [
"JMSNRSCF_mystery12264_s01.fastq.gz",
"JMSNRSCF_mystery12264_s02.fastq.gz",
"JMSNRSCF_mystery12264_s03.fastq.gz",
"JMSNRSCF_mystery12264_s04.fastq.gz"
]
},
"@mystery17075": {
"LB": "mystery17075",
"barcode": [
"GTGGCC"
],
"output": [
"JMSNRSCF_mystery17075_s01.fastq.gz",
"JMSNRSCF_mystery17075_s02.fastq.gz",
"JMSNRSCF_mystery17075_s03.fastq.gz",
"JMSNRSCF_mystery17075_s04.fastq.gz"
]
},
"@mystery4368": {
"LB": "mystery4368",
"barcode": [
"CGCCTG"
],
"output": [
"JMSNRSCF_mystery4368_s01.fastq.gz",
"JMSNRSCF_mystery4368_s02.fastq.gz",
"JMSNRSCF_mystery4368_s03.fastq.gz",
"JMSNRSCF_mystery4368_s04.fastq.gz"
]
},
"@mystery4895": {
"LB": "mystery4895",
"barcode": [
"GGGGGG"
],
"output": [
"JMSNRSCF_mystery4895_s01.fastq.gz",
"JMSNRSCF_mystery4895_s02.fastq.gz",
"JMSNRSCF_mystery4895_s03.fastq.gz",
"JMSNRSCF_mystery4895_s04.fastq.gz"
]
},
"@mystery8619": {
"LB": "mystery8619",
"barcode": [
"AGTTCC"
],
"output": [
"JMSNRSCF_mystery8619_s01.fastq.gz",
"JMSNRSCF_mystery8619_s02.fastq.gz",
"JMSNRSCF_mystery8619_s03.fastq.gz",
"JMSNRSCF_mystery8619_s04.fastq.gz"
]
},
"@mystery9788": {
"LB": "mystery9788",
"barcode": [
"CCGTCC"
],
"output": [
"JMSNRSCF_mystery9788_s01.fastq.gz",
"JMSNRSCF_mystery9788_s02.fastq.gz",
"JMSNRSCF_mystery9788_s03.fastq.gz",
"JMSNRSCF_mystery9788_s04.fastq.gz"
]
}
},
"confidence threshold": 0.95,
"noise": 0.05,
"transform": {
"token": [
"1::6"
]
},
"undetermined": {
"output": [
"JMSNRSCF_undetermined_s01.fastq.gz",
"JMSNRSCF_undetermined_s02.fastq.gz",
"JMSNRSCF_undetermined_s03.fastq.gz",
"JMSNRSCF_undetermined_s04.fastq.gz"
]
}
},
"template": {
"transform": {
"token": [
"0::",
"3::"
]
}
}
}
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