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
|
#!/usr/bin/env cwl-runner
id: InputSecondaryFileConformanceTest
class: CommandLineTool
cwlVersion: v1.2
doc: |
Simple test to confirm the implementation of expressions returning a File within a CommandInputParameter.secondaryFile field.
Use GREP to filter the result from ls to ensure we only get the secondary files in there.
Related links:
- Issue: https://github.com/common-workflow-language/cwltool/issues/1232
- PR: https://github.com/common-workflow-language/cwltool/pull/1233
- Discourse: https://cwl.discourse.group/t/ask-cwl-to-rename-a-secondary-file/72
inputs:
- id: inputWithSecondary
type: File
doc: |
This input will with a secondary file `.accessory`. You could create these files (and its accessory) with:
```bash
touch secondary_file_test.txt
touch secondary_file_test.txt.accessory
```
secondaryFiles:
- |
${
function resolveSecondary(base, secPattern) {
if (secPattern[0] == '^') {
var spl = base.split('.');
var endIndex = spl.length > 1 ? spl.length - 1 : 1;
return resolveSecondary(spl.slice(undefined, endIndex).join("."), secPattern.slice(1));
}
return base + secPattern;
}
return [{
"class": "File",
"location": inputs.accessory.location,
"basename": resolveSecondary(self.basename, '^.accessory')
}];
}
- id: accessory
type: File
arguments:
- "ls"
- $(inputs.inputWithSecondary.dirname)
- valueFrom: "|"
shellQuote: false
- "grep"
- "secondary"
outputs:
- id: output_file
type: stdout
stdout: result
requirements:
InlineJavascriptRequirement: {}
ShellCommandRequirement: {}
|
