common-workflow-language / common-workflow-language/cwltool

'format' key in input YAML interpreted as file

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#568 3 comments 2 reactions 0 assignees View on GitHub
bug
Dominant language
Python
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2d 7h
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Description

When the input file is a YAML that contains a key named 'format', then it is interpreted as file.

## Workflow Code

Workflow, echo.cwl:
```
cwlVersion: v1.0
class: CommandLineTool
baseCommand: echo

inputs:
format:
type: string
inputBinding:
position: 1

outputs:
output: stdout
```

Input YAML, hello_world.yaml:
```
format: Hello world
```

Usage:
```
cwltool echo.cwl hello_world.yaml
```

## Expected Behavior
The output file should contain the string: 'Hello world'.
Similar to cwltool echo.cwl --format 'Hello world'

## Actual Behavior
Output file contains a path to a file: file:///path/to/working/directory/Hello world

## Your Environment
* cwltool version: 1.0.20170928192020

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