sprm/pipeline.cwl at main · hubmapconsortium/sprm · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.1
label: SPRM pipeline

inputs:
  image_dir:
    label: "Directory containing image files"
    type: Directory
  mask_dir:
    label: "Directory containing mask files"
    type: Directory
  options_file:
    label: "SPRM options file"
    type: File?
  cell_types_directory:
    label: "Cell type annotations file"
    type: Directory[]?
  options_preset:
    label: "SPRM options preset (alternate options file bundled with the package)"
    type: string?
  enable_manhole:
    label: "Whether to enable remote debugging via 'manhole'"
    type: boolean?
  enable_faulthandler:
    label: "Whether to enable the Python 'faulthandler' module"
    type: boolean?
  threadpool_limit:
    label: "Whether to enable the Python 'faulthandler' module"
    type: int?
  verbose:
    label: "Whether to enable verbose/debug mode"
    type: boolean?
  min_memory:
    label: "Whether to conserve memory by leaving large arrays on disk"
    type: boolean?
  processes:
    label: "Number of images to process in parallel (default: 1)"
    type: int?
  num_dims:
    label: "Number of dimensions associated with the data"
    type: int?

outputs:
  sprm_output:
    outputSource: sprm/output_dir
    type: Directory
    label: "SPRM output"
  sdata_zarrs:
    outputSource: create_spatial_data/sdata_zarrs
    type: Directory[]

steps:
  ome_tiff_normalize_expr:
    in:
      data_dir:
        source: image_dir
    out: [output_dir]
    run: ome-tiff-normalize/ome_tiff_normalize.cwl
  ome_tiff_normalize_mask:
    in:
      data_dir:
        source: mask_dir
    out: [output_dir]
    run: ome-tiff-normalize/ome_tiff_normalize.cwl
  sprm:
    in:
      image_dir:
        source: ome_tiff_normalize_expr/output_dir
      mask_dir:
        source: ome_tiff_normalize_mask/output_dir
      options_file:
        source: options_file
      cell_types_directory:
        source: cell_types_directory
      options_preset:
        source: options_preset
      enable_manhole:
        source: enable_manhole
      enable_faulthandler:
        source: enable_faulthandler
      threadpool_limit:
        source: threadpool_limit
      verbose:
        source: verbose
      min_memory:
        source: min_memory
      processes:
        source: processes
    out: [output_dir]
    run: steps/sprm.cwl
    label: "SPRM analysis"
  create_spatial_data:
    in:
      image_dir:
        source: ome_tiff_normalize_expr/output_dir
      mask_dir:
        source: ome_tiff_normalize_mask/output_dir
      sprm_dir:
        source: sprm/output_dir
      num_dims:
        source: num_dims
    out: [sdata_zarrs]
    run: steps/create-spatial-data.cwl
    label: "Conversion to spatialdata format"