openproblems/src/reporting/combine_output/config.vsh.yaml at e8119ce8ff1e0426157b1580d5b4601659bc87d3 · openproblems-bio/openproblems · 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
name: combine_output
namespace: reporting
description: Combine task outputs into a single JSON

argument_groups:
  - name: Inputs
    arguments:
      - name: --input_task_info
        type: file
        description: Task info file
        info:
          format:
            type: json
            schema: /common/schemas/results_v4/task_info.json
        required: true
        example: resources_test/openproblems/task_results_v4/processed/task_info.json
      - name: --input_dataset_info
        type: file
        description: Dataset info file
        info:
          format:
            type: json
            schema: /common/schemas/results_v4/dataset_info.json
        required: true
        example: resources_test/openproblems/task_results_v4/processed/dataset_info.json
      - name: --input_method_info
        type: file
        description: Method info file
        info:
          format:
            type: json
            schema: /common/schemas/results_v4/method_info.json
        required: true
        example: resources_test/openproblems/task_results_v4/processed/method_info.json
      - name: --input_metric_info
        type: file
        description: Metric info file
        info:
          format:
            type: json
            schema: /common/schemas/results_v4/metric_info.json
        required: true
        example: resources_test/openproblems/task_results_v4/processed/metric_info.json
      - name: --input_results
        type: file
        description: Results file
        info:
          format:
            type: json
            schema: /common/schemas/results_v4/results.json
        required: true
        example: resources_test/openproblems/task_results_v4/processed/results.json
      - name: --input_quality_control
        type: file
        description: Quality control file
        info:
          format:
            type: json
            schema: /common/schemas/results_v4/quality_control.json
        required: true
        example: resources_test/openproblems/task_results_v4/processed/quality_control.json

  - name: Outputs
    arguments:
    - name: --output
      type: file
      direction: output
      description: Combined output JSON
      default: combined_output.json
      info:
        format:
          type: json
          schema: /common/schemas/results_v4/combined_output.json

resources:
  - type: r_script
    path: script.R
  - path: /common/schemas
    dest: schemas

test_resources:
  - type: python_script
    path: /common/component_tests/run_and_check_output.py
  - path: /resources_test/openproblems/task_results_v4
    dest: resources_test/openproblems/task_results_v4

engines:
  - type: docker
    image: openproblems/base_r:1
    setup:
      - type: apt
        packages:
        - nodejs
        - npm
      - type: docker
        run: npm install -g ajv-cli

runners:
  - type: executable
  - type: nextflow
    directives:
      label: [lowmem, lowtime, lowcpu]