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**PGAP is not running when I use my own data**
I successfully ran the M. genitalium test genome but when I try to run my own genome it says "PGAP failed, docker exited with rc = 1".
I have attache…
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Hi, when I run the SE pipeline (cwltool --debug ./cwl/wf_get_peaks_scatter_se.cwl single_end_clip.yml ), I get the following error after make_bigwigs:
DEBUG [job make_bigwigs] initial work dir {
…
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> Traceback (most recent call last):
> File "/bin/correlation.py", line 43, in
> main()
> File "/bin/correlation.py", line 19, in main
> rna = pd.read_csv(opts.rnafile, sep='\t', inde…
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**Describe the bug**
When running the pipeline with the CLI, an attempt is made to download a file where no file is specified in the input
**To Reproduce**
git clone https://github.com/hubmapconsorti…
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As discussed on Gitter with Michael Crusoe.
I have an issue with some output files having a wrong name, which only occurs on some machines. One of the outputs has a trailing `_2` in its filename. I t…
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workflow:
```
class: Workflow
cwlVersion: v1.0
id: test
label: test
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: sample
type: 'string[]?'
default:
- …
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I am running pgap on plasmid sequences. It completed successfully with the --ignore-all-errors flag, and works successfully on the trial genome as well. However I will be submitting the sequences to N…
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### Bug description
A class type used as key for a dict is valid, but is incorrectly reported as unhashable.
See Expected Behavior for example.
### Configuration
https://github.com/crim-c…
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Trying to read [the DeepHealth tissue/tumor prediction workflow](https://github.com/crs4/deephealth-pipelines/blob/0d09bc091e1f7a9778e4286a22db9e9f8d96a315/cwl/predictions.cwl) leads to a crash:
``…
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The `run.py` script and `run-json.py` scripts should be deprecated, along with the `operator` sections, in lieu of using the `cwltool` and Toil built-in CLI args to supply CWL inputs
Migrate the in…