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

New cwltool error on basic gzip job

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#130 0 comments 0 reactions 1 assignee Claimed by @manu-chroma View on GitHub
Dominant language
Python
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Merged PRs (30d)
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Description

_gzip.cwl_

```
cwlVersion: cwl:draft-3
class: CommandLineTool
baseCommand: [gzip, -f]
inputs:
- id: input_file
type: File
inputBinding:
position: 1
outputs:
- id: gzipped_file
type: File
outputBinding:
glob: "*.gz"
```

_gzip-job.yml_

```
input_file:
class: File
path: foo.txt
```

"Did not find output" error:

```
$ cwltool gzip.cwl gzip-job.yml
/home/jiayong2/miniconda2/bin/cwltool 1.0.20160714182449
[job gzip.cwl] /tmp/tmptj_yvK$ gzip \
-f \
/tmp/tmpSu82rH/stga02c04cd-1755-4ee1-a3f8-fd830fd1d62a/foo.txt
Error while running job: Error collecting output for parameter 'gzipped_file': Did not find output file with glob pattern: '['*.gz']'
[job gzip.cwl] completed permanentFail
Final process status is permanentFail
Workflow error, try again with --debug for more information:
Process status is ['permanentFail']
```

But it works on an earlier version

```
$ cwltool gzip.cwl gzip-job.yml
/home/jiayong/miniconda2/bin/cwltool 1.0.20160427142240
[job 140300885704848] /home/jiayong/cwl/test/gzip$ gzip /home/jiayong/cwl/test/gzip/foo.txt
Final process status is success
{
"gzipped_file": {
"size": 33,
"path": "/home/jiayong/cwl/test/gzip/foo.txt.gz",
"checksum": "sha1$51fd16e775a790abd6174fd6d111300248c99761",
"class": "File"
}
}
```

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