sdk/cwl/tests/chipseq/chip-seq-single.json

   1 {
   2     "referenceGenomeSequence": {
   3         "class": "File",
   4         "location": "data/Genomes/Homo_sapiens/GRCh38.p2/WholeGenome/genome.fa",
   5         "metadata": {
   6             "reference_genome": {
   7                 "organism": "Homo sapiens",
   8                 "version": "hg38"
   9             },
  10             "annotation": {
  11                 "source": "gencode",
  12                 "version": "v24"
  13             }
  14         }
  15     },
  16     "referenceGenomeSequenceDrosophila": {
  17         "class": "File",
  18         "location": "data/Genomes/Drosophila_melanogaster/dmel_r6.16/WholeGenome/genome.fa",
  19         "metadata": {
  20             "reference_genome": {
  21                 "organism": "Drosophila melanogaster",
  22                 "version": "rmel_r6.16"
  23             }
  24         }
  25     },
  26     "blacklistBed": {
  27         "class": "File",
  28         "location": "data/Genomes/Blacklist/lists2/hg38-blacklist.v2.bed",
  29         "metadata": {
  30             "reference_genome": {
  31                 "organism": "Homo sapiens",
  32                 "version": "hg38"
  33             },
  34             "annotation": {
  35                 "source": "gencode",
  36                 "version": "v24"
  37             }
  38         }
  39     },
  40     "BowtieHumanReference": {
  41         "class": "Directory",
  42         "location": "data/Genomes/Homo_sapiens/GRCh38.p2/Bowtie2Index/",
  43         "metadata": {
  44             "reference_genome": {
  45                 "organism": "Homo sapiens",
  46                 "version": "hg38"
  47             },
  48             "annotation": {
  49                 "source": "gencode",
  50                 "version": "v24"
  51             }
  52         }
  53     },
  54     "BowtieDrosophilaReference": {
  55         "class": "Directory",
  56         "location": "data/Genomes/Drosophila_melanogaster/dmel_r6.16/Bowtie2Index/",
  57         "metadata": {
  58             "reference_genome": {
  59                 "organism": "Drosophila melanogaster",
  60                 "version": "rmel_r6.16"
  61             }
  62         }
  63     },
  64     "sampleName": "LED054_0p03nMR1.0",
  65     "inputFastq1": {
  66         "class": "File",
  67         "metadata": {
  68             "user": "kmavrommatis",
  69             "sample_id": [
  70                2
  71             ]
  72         },
  73         "location": "DATEST/ChIP-Seq/Raw/fastq/Input_R1.fastq.gz",
  74         "secondaryFiles": []
  75     },
  76     "inputFastq2": {
  77         "class": "File",
  78         "metadata": {
  79             "user": "kmavrommatis",
  80             "sample_id": [
  81                 2
  82             ]
  83         },
  84         "location": "DATEST/ChIP-Seq/Raw/fastq/Input_R3.fastq.gz",
  85         "secondaryFiles": []
  86     },
  87     "inputFastqUMI": {
  88         "class": "File",
  89         "metadata": {
  90             "user": "kmavrommatis",
  91             "sample_id": [
  92                2
  93             ]
  94         },
  95         "location": "DATEST/ChIP-Seq/Raw/fastq/Input_R2.fastq.gz",
  96         "secondaryFiles": []
  97     }
  98 }
  99