sdk/cwl/tests/chipseq/cwl-packed.json

   1 {
   2     "$graph": [
   3         {
   4             "class": "Workflow",
   5             "id": "#main",
   6             "doc": "Pipeline that is applied on single ChIP-seq samples.\n\nStarts with QC on the reads and trimming (for adapters and based on quality)\n\nAligns to human genome and adds UMI\n\nAligns to Drosophila genome and counts the number of reads.\n\nAfter the alignment to human genome the files are filtered for duplicates, multimappers and alignments in black listed regions",
   7             "label": "ChIP-Seq (single sample)",
   8             "inputs": [
   9                 {
  10                     "id": "#inputFastq1",
  11                     "type": "File",
  12                     "https://www.sevenbridges.com/fileTypes": "fastq",
  13                     "https://www.sevenbridges.com/x": 0,
  14                     "https://www.sevenbridges.com/y": 1726.25
  15                 },
  16                 {
  17                     "id": "#blacklistBed",
  18                     "type": "File",
  19                     "https://www.sevenbridges.com/x": 746.4744873046875,
  20                     "https://www.sevenbridges.com/y": 1903.265625
  21                 },
  22                 {
  23                     "id": "#referenceGenomeSequence",
  24                     "type": "File",
  25                     "secondaryFiles": [
  26                         ".fai",
  27                         "^.dict"
  28                     ],
  29                     "https://www.sevenbridges.com/fileTypes": "fasta, fa",
  30                     "https://www.sevenbridges.com/x": 0,
  31                     "https://www.sevenbridges.com/y": 1405.203125
  32                 },
  33                 {
  34                     "id": "#sampleName",
  35                     "type": "string",
  36                     "https://www.sevenbridges.com/x": 0,
  37                     "https://www.sevenbridges.com/y": 1191.171875
  38                 },
  39                 {
  40                     "id": "#inputFastq2",
  41                     "type": [
  42                         "null",
  43                         "File"
  44                     ],
  45                     "https://www.sevenbridges.com/fileTypes": "fastq",
  46                     "https://www.sevenbridges.com/x": 0,
  47                     "https://www.sevenbridges.com/y": 1619.234375
  48                 },
  49                 {
  50                     "id": "#inputFastqUMI",
  51                     "type": "File",
  52                     "https://www.sevenbridges.com/x": 0,
  53                     "https://www.sevenbridges.com/y": 1512.21875
  54                 },
  55                 {
  56                     "id": "#BowtieHumanReference",
  57                     "type": "Directory",
  58                     "https://www.sevenbridges.com/x": 363.875,
  59                     "https://www.sevenbridges.com/y": 1519.21875
  60                 },
  61                 {
  62                     "id": "#BowtieDrosophilaReference",
  63                     "type": "Directory",
  64                     "https://www.sevenbridges.com/x": 363.875,
  65                     "https://www.sevenbridges.com/y": 1626.234375
  66                 },
  67                 {
  68                     "id": "#referenceGenomeSequenceDrosophila",
  69                     "type": "File",
  70                     "secondaryFiles": [
  71                         ".fai"
  72                     ],
  73                     "https://www.sevenbridges.com/x": 0,
  74                     "https://www.sevenbridges.com/y": 1298.1875
  75                 }
  76             ],
  77             "outputs": [
  78             ],
  79             "steps": [
  80                 {
  81                     "id": "#step1",
  82                     "in": {
  83                         "inp": "#inputFastq1"
  84                     },
  85                     "out": [],
  86                     "run": "../cat.cwl"
  87                 }
  88             ],
  89             "requirements": [
  90             ]
  91         },
  92    ],
  93     "cwlVersion": "v1.0"
  94 }