common-workflow-language / common-workflow-language/cwltool
Not possible to pack workflow A with reference to packed workflow B
- Dominant language
- Python
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- 376
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- 2d 7h
- Merged PRs (30d)
- 12
Description
## Expected Behavior
We have a workflow A with reference to another workflow B that been packed. The task is to use ```--pack``` to that workflow A.
## Actual Behavior
It throws an error.
## Workflow Code
```
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: SubworkflowFeatureRequirement
inputs:
in_file: File
outputs:
output_bam:
type: File
outputSource: use_packed_pipe/output_sorted_bam
steps:
use_packed_pipe:
run: https://raw.githubusercontent.com/prefabsprout/Bioinf_scripts/master/packed_pipe.cwl
in:
main/in_file: in_file
out: [ output_sorted_bam ]
```
## Full Traceback
Command: ```cwltool --debug --pack use_packed_pipe.cwl```
```
ERROR I'm sorry, I couldn't load this CWL file.
The error was:
Traceback (most recent call last):
File "/home/stepan/.local/lib/python3.6/site-packages/cwltool/main.py", line 952, in main
stdout.write(print_pack(loadingContext, uri))
File "/home/stepan/.local/lib/python3.6/site-packages/cwltool/main.py", line 587, in print_pack
packed = pack(loadingContext, uri)
File "/home/stepan/.local/lib/python3.6/site-packages/cwltool/pack.py", line 256, in pack
v = rewrite[r]
KeyError: 'https://raw.githubusercontent.com/prefabsprout/Bioinf_scripts/master/packed_pipe.cwl#sam_to_bam.cwl'
```
## Your Environment
* cwltool version
3.0.20200710214758
## Used files
[packed_pipeline_files.zip](https://github.com/common-workflow-language/cwltool/files/4924032/packed_pipeline_files.zip)
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