|
1 | | -# |
2 | | -# This is a not quite so funked out workflow |
3 | | -# |
| 1 | +cwlVersion: v1.0 |
4 | 2 | class: Workflow |
5 | | -description: "Reverse the lines in a document, then sort those lines." |
6 | | -cwlVersion: cwl:draft-3 |
7 | | - |
8 | | -# Requirements & hints specify prerequisites and extensions to the workflow. |
9 | | -# In this example, DockerRequirement specifies a default Docker container |
10 | | -# in which the command line tools will execute. |
11 | | -hints: |
12 | | - - class: DockerRequirement |
13 | | - dockerPull: debian:8 |
14 | | - |
15 | | - |
16 | | -# The inputs array defines the structure of the input object that describes |
17 | | -# the inputs to the workflow. |
18 | | -# |
19 | | -# The "reverse_sort" input parameter demonstrates the "default" field. If the |
20 | | -# field "reverse_sort" is not provided in the input object, the default value will |
21 | | -# be used. |
22 | 3 | inputs: |
23 | | - - id: input |
24 | | - type: File |
25 | | - description: "The input file to be processed." |
26 | | - - id: reverse_sort |
27 | | - type: boolean |
28 | | - default: true |
29 | | - description: "If true, reverse (decending) sort" |
| 4 | + inp: File |
| 5 | + ex: string |
30 | 6 |
|
31 | | -# The "outputs" array defines the structure of the output object that describes |
32 | | -# the outputs of the workflow. |
33 | | -# |
34 | | -# Each output field must be connected to the output of one of the workflow |
35 | | -# steps using the "connect" field. Here, the parameter "#output" of the |
36 | | -# workflow comes from the "#sorted" output of the "sort" step. |
37 | 7 | outputs: |
38 | | - - id: output |
| 8 | + classout: |
39 | 9 | type: File |
40 | | - source: "#sorted/output" |
41 | | - description: "The output with the lines reversed and sorted." |
| 10 | + outputSource: compile/classfile |
42 | 11 |
|
43 | | -# The "steps" array lists the executable steps that make up the workflow. |
44 | | -# The tool to execute each step is listed in the "run" field. |
45 | | -# |
46 | | -# In the first step, the "inputs" field of the step connects the upstream |
47 | | -# parameter "#input" of the workflow to the input parameter of the tool |
48 | | -# "revtool.cwl#input" |
49 | | -# |
50 | | -# In the second step, the "inputs" field of the step connects the output |
51 | | -# parameter "#reversed" from the first step to the input parameter of the |
52 | | -# tool "sorttool.cwl#input". |
53 | 12 | steps: |
54 | | - - id: rev |
55 | | - inputs: |
56 | | - - { id: input, source: "#input" } |
57 | | - outputs: |
58 | | - - { id: output } |
59 | | - run: revtool.cwl |
| 13 | + untar: |
| 14 | + run: tar-param.cwl |
| 15 | + in: |
| 16 | + tarfile: inp |
| 17 | + extractfile: ex |
| 18 | + out: [example_out] |
60 | 19 |
|
61 | | - - id: sorted |
62 | | - inputs: |
63 | | - - { id: input, source: "#rev/output" } |
64 | | - - { id: reverse, source: "#reverse_sort" } |
65 | | - outputs: |
66 | | - - { id: output } |
67 | | - run: sorttool.cwl |
| 20 | + compile: |
| 21 | + run: arguments.cwl |
| 22 | + in: |
| 23 | + src: untar/example_out |
| 24 | + out: [classfile] |
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