User: peter.amstutz

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peter.amstutz300
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@peteramstutz
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Posts by peter.amstutz

<prev • 18 results • page 1 of 2 • next >
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Answer: A: Is there a schema for CWL inputs/job files?
... To expand a bit on what Michael said, the "inputs" and "outputs" section of every tool or workflow is a schema for the input object, so (although I have not tried it) it probably is not much more complicated than dumping the inputs section and using the code generator on it. ...
written 4 months ago by peter.amstutz300
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Comment: C: Combine subject with sample type in a scatter?
... Try adding "subjectName" to inputs and then referring to it this way: valueFrom: "$(inputs.subjectName)_$(self.sample)" ...
written 5 months ago by peter.amstutz300
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Answer: A: help identifying bioinformatics operations tools
... Maybe something like TranSMART https://transmartfoundation.org/scientists-clinicians/ for patient management and Arvados http://arvados.org for sequencing data management & analysis? ...
written 10 months ago by peter.amstutz300
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Answer: A: CWL: Setting output directories for steps in a workflow
... cwltool has an option --leave-outputs: "Leave output files in intermediate output directories." This may not be quite what you want, though. You can use an ExpressionTool to take a group of files and produce a Directory object. This looks like: cwlVersion: v1.0 class: ExpressionTool requirement ...
written 2.6 years ago by peter.amstutz300
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Answer: A: Reference implementation seems to reject step without inputs
... You need to provide an "in" section with an empty list. Also "id: gradients" is redundant: gradients: run: tools/gradients_gen.cwl in: [] out: [fill_gradient, highlight_gradient] However you're right, as a general rule, fields which can accept empty lists should be opt ...
written 2.8 years ago by peter.amstutz300
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Comment: C: Using the Directory type in Common Workflow Language
... To follow up, I have a PR which correctly adds the Directory path to the command line as intended: https://github.com/common-workflow-language/cwltool/pull/144 ...
written 3.2 years ago by peter.amstutz300
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Comment: C: Using the Directory type in Common Workflow Language
... Hi Peter, I think this is a bug. It's supposed to add the directory path to the command line, but that doesn't seem to be happening here. I'll look into it. ...
written 3.2 years ago by peter.amstutz300
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Comment: C: How to specify an optional input for a complex type in CWL?
... Your second approach should be the correct one. Can you provide the error when you try it that way? ...
written 3.3 years ago by peter.amstutz300
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Comment: C: Minimal CWL (Common Workflow Language) workflow from Makefile
... The second one.  It's a specification for a declarative document format for describing portable workflows.  The goal is to have lots of interoperable implementations. ...
written 4.2 years ago by peter.amstutz300
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Comment: C: Minimal CWL (Common Workflow Language) workflow from Makefile
... "EDIT: feel free to add the file for your favorite workflow-engine as an answer." That's right, that's nextflow.io. ...
written 4.2 years ago by peter.amstutz300

Latest awards to peter.amstutz

Scholar 4 months ago, created an answer that has been accepted. For A: Minimal CWL (Common Workflow Language) workflow from Makefile
Scholar 2.8 years ago, created an answer that has been accepted. For A: Minimal CWL (Common Workflow Language) workflow from Makefile
Appreciated 2.9 years ago, created a post with more than 5 votes. For A: List Of Cloud Genomics Companies
Good Answer 3.6 years ago, created an answer that was upvoted at least 5 times. For A: List Of Cloud Genomics Companies
Appreciated 4.2 years ago, created a post with more than 5 votes. For A: List Of Cloud Genomics Companies
Scholar 4.2 years ago, created an answer that has been accepted. For A: Minimal CWL (Common Workflow Language) workflow from Makefile
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Minimal CWL (Common Workflow Language) workflow from Makefile
Scholar 4.2 years ago, created an answer that has been accepted. For A: Minimal CWL (Common Workflow Language) workflow from Makefile
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: List Of Cloud Genomics Companies
Teacher 4.7 years ago, created an answer with at least 3 up-votes. For A: List Of Cloud Genomics Companies

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