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As detailed in https://github.com/dockstore/dockstore/issues/5594, some workflow engines, including miniwdl and Cromwell, fail to run a valid Dockstore workflow when:
* the workflow is referenced v…
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```
File "/home/michael/src/galaxy-cwl/lib/galaxy/tools/__init__.py", line 1780, in handle_single_execution
rval = self.execute(
File "/home/michael/src/galaxy-cwl/lib/galaxy/tools/__init__…
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For the EDAM ontology, seeing `http://edamontology.org/format_2572` is confusing. Seeing `BAM` makes a lot more sense. We should display the name of these words and not the IDs.
Edit: This is true wi…
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We have a workflow for instance with 2 steps. First step (indexing) is creating a bunch of files which are required for the successful execution of the next step (alignment).
The main issue is the un…
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It is difficult to get to the specifications of the individual versions, there should be a link from the user guide to the Common Workflow Language (CWL) Command Line Tool Description. Searching for s…
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We would like to run containers safely in a multi-user LSF cluster. Docker has many security issues stemming from dockerd being run as root. Singularity is an alternative that gains more and more popu…
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**Issue by [mr-c](https://github.com/mr-c)**
_Wednesday Sep 05, 2018 at 11:19 GMT_
_Originally opened as https://github.com/clap-rs/clap/issues/1337_
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### Bug or Feature Request Summary
Spec…
epage updated
2 years ago
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Following on from issue #278, the purpose of this issue is to capture examples of workflows from the various approaches (OpenEO, OAPIP Part 3, etc.), compare them and see where there is commonality an…
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I'm trying to fix `toil-container`, with reference to #1768. One key aspect to this is being able to set `--singularity` or `--docker` on the command line, storing that in the Toil options, and then c…
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Hi, I’m responsible for GATK docs and just came across this project; it seems like a really useful thing for GATK users and we’d like to support it as much as we can. Full disclosure, we’re working on…