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Workflow Administrator:
`Submission 9683420 failed. The workflow description is: WorkflowJobImpl [submissionId=null, containerName=workflow_job.95aa5e0d-9a4f-4c96-85d2-182b8010ad5c, container=com.…
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## Expected Behavior
cwltool should handle an input type such as the following:
type:
- 'null'
- type: enum
symbols: ['across', 'commas','long']
## Actual Behavior
As of rel…
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According to the [spec](https://www.commonwl.org/v1.0/CommandLineTool.html#Runtime_environment), `runtime.outdir` is an absolute path to the designated output directory.
For example, let us conside…
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lsb_release -a
--->
LSB Version: n/a
Distributor ID: ManjaroLinux
Description: Manjaro Linux
Release: 18.0.0-rc
Codename: Illyria
git clone git@github.com:EOSC-LOFAR/prefactor-cwl.git …
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## Bug Report
See screenshot of a hosted WDL workflow:
![screen shot 2018-10-11 at 3 23 35 pm](https://user-images.githubusercontent.com/1049340/46837335-d1356e00-cd69-11e8-8664-60156693d997.png…
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Our group also cannot run docker on our cluster and have tried using Singularity and conda environments. We've managed to get the test genome that comes as part of the docker to complete, however when…
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https://github.com/common-workflow-language/cwltool/blob/734322eb5677717c5836eed361823f0a585e5de1/cwltool/process.py#L310
To reproduce: run `cwltool --outdir ${HOME}` and a simple CWL description o…
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Dear Bcbio team,
I tried installing Mutect 1.1.7 and gatk 3.4 as per below instructions under section "GATK and MuTect/MuTect"
https://bcbio-nextgen.readthedocs.io/en/latest/contents/installation.…
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Dear All,
I am running my CWL workflow on python 2.7 environment.
I am trying to run couple python scripts, on BAM and tsv files. While I try to run my script. It is throwing following error. Follo…
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The idea is from the problem that we can't extract the identifiers of the inputs/outputs to the **workflow** from the cwltool debug output.
For example, in the workflow file `revsort.cwl` of the co…