User: peter.amstutz

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peter.amstutz270
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Posts by peter.amstutz

<prev • 16 results • page 1 of 2 • next >
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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 19 days ago by peter.amstutz270
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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 21 months ago by peter.amstutz270
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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 2.0 years ago by peter.amstutz270
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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 2.4 years ago by peter.amstutz270
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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 2.4 years ago by peter.amstutz270
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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 2.5 years ago by peter.amstutz270
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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 3.4 years ago by peter.amstutz270
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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 3.4 years ago by peter.amstutz270
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Answer: A: Minimal CWL (Common Workflow Language) workflow from Makefile
... Responded with an example on this github issue:  https://github.com/common-workflow-language/workflows/issues/1 ...
written 3.4 years ago by peter.amstutz270
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Comment: C: Minimal CWL (Common Workflow Language) workflow from Makefile
... Responded with an example on this github issue:  https://github.com/common-workflow-language/workflows/issues/1 ...
written 3.4 years ago by peter.amstutz270

Latest awards to peter.amstutz

Scholar 2.0 years ago, created an answer that has been accepted. For A: Minimal CWL (Common Workflow Language) workflow from Makefile
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: List Of Cloud Genomics Companies
Good Answer 2.8 years ago, created an answer that was upvoted at least 5 times. For A: List Of Cloud Genomics Companies
Appreciated 3.4 years ago, created a post with more than 5 votes. For A: List Of Cloud Genomics Companies
Scholar 3.4 years ago, created an answer that has been accepted. For A: Minimal CWL (Common Workflow Language) workflow from Makefile
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Minimal CWL (Common Workflow Language) workflow from Makefile
Scholar 3.4 years ago, created an answer that has been accepted. For A: Minimal CWL (Common Workflow Language) workflow from Makefile
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: List Of Cloud Genomics Companies
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: List Of Cloud Genomics Companies

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