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Hi,
to get singularity to run, I've had to go into almost all cwl scripts and put "#!/usr/bin/env -S cwltool --singularity" at the top.
Now, I STILL get a problem where it's trying to call Docke…
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this works:
```
cwlVersion: v1.0
class: CommandLineTool
baseCommand: env
requirements:
EnvVarRequirement:
envDef:
HELLO: hi
inputs: []
outputs: []
```
but if i change it to
`…
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When I run the following command with the latest version of `cwltool`:
```bash
$ cwltool https://sandbox.zenodo.org/record/1016630/files/trimming_and_qc.cwl --help
```
I encounter the error be…
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From @aniewielska
> if this [`self.max_cores = float(psutil.cpu_count())`] is what is propagated to TES request, then this does not have much sense, if TES is remote (and it also affects the execut…
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Hi Yoshiaki,
After my previous issue with memory requirements and not being able to edit this in the wrapper script (I don't understand Docker very well), now I cannot even seem to use Singularity …
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Currently cwltool does not support the following CWL document.
nestedTypeDSL.cwl
```cwl
cwlVersion: v1.2
class: CommandLineTool
baseCommand: echo
inputs:
inp: File[][]
outputs: []
```
…
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Hi,
when I tried testing this pipeline using the demo in the READMe, an error occurred:
"
URI prefix 's' of 's:Organization' not recognized, are you missing a $namespaces section?
URI prefix 's' o…
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See https://github.com/common-workflow-language/cwltool/pull/74 & https://github.com/common-workflow-language/cwltool/pull/106
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A variation on the `cwltool` specific experimental extension for "secret" parameters https://github.com/common-workflow-language/cwltool/pull/683
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If you have a CWL file of:
```yaml
cwlVersion: v1.0
class: CommandLineTool
inputs:
param:
type:
type: array
items: string[]
outputs: []
```
and run cwltool:
```
$ cw…