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We need to rationalize the provision of configuration options to stages somewhat - right now it is a bit confused - the pipeline both reads the yaml config file and passes all the options in it on the…
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I'm trying to run a CWL runner via Xenon, which writes a description of the results produced on stdout. This works fine with SLURM, but when using Torque, Xenon complains that it cannot set the standa…
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## Bug Report
Dockstore interface doesn't support `$include`, `$import` and `$mixin` to populate sections.
I've used it in the doc section:
```cwl
doc:
$include: includes/doc.yml
```
…
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## Feature Request
### Desired behaviour
Expand affliates for Dockstore
- UCSC should be added alongside OICR and GA4GH
Contributor section should be added as a prominent link below our affli…
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Hi, I have a somatic mutation filtered VCF file generated by GATK haplotypeCaller. I used that file to run MuPeXI on the web server, but got the following errors. Could you please let me know what's w…
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Hi Brad,
I'm trying to get the bcbio CWL implementation to work, but I keep running into the following error:
```
$ bcbio_vm.py cwl config/bcbio_cwl.yaml …
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https://www.synapse.org/#!Synapse:syn8507133/wiki/415976
This would show whether our workflow is reproducible.
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```
The error was: 'ascii' codec can't encode character u'\u2019' in position 9238: ordinal not in range(128)
```
From https://view.commonwl.org/workflows/github.com/MG-RAST/amplicon/blob/wilke/c…
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```
$ .virtualenv/bin/cwltool ndppp_prep_cal.cwl --msin data/L591513_SB000_uv.MS
.virtualenv/bin/cwltool 1.0.20171017195544
Resolved 'ndppp_prep_cal.cwl' to 'file:///home/gijs/prefactor-cwl/ndppp_p…