User: karl.sebby

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karl.sebby70
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Posts by karl.sebby

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Answer: A: Is there a schema for CWL inputs/job files?
... Here's what I ended up with and has been working for the cases I've tested so far. $base: "https://w3id.org/cwl/cwl#" $namespaces: cwl: "https://w3id.org/cwl/cwl#" sld: "https://w3id.org/cwl/salad#" rdfs: "http://www.w3.org/2000/01/rdf-schema#" $graph: ...
written 8 months ago by karl.sebby70
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Comment: C: Is there a schema for CWL inputs/job files?
... Awesome! I'll give this a try and then try out some File and Directory inputs. ...
written 9 months ago by karl.sebby70
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Comment: C: Is there a schema for CWL inputs/job files?
... OK. So I've gotten around to giving this a try and I'm hitting some issues. To keep things simple I'm playing around with the echo example, 1st-tool.cwl, and echo-job.yml used in the user guide https://github.com/common-workflow-language/user_guide/tree/gh-pages/_includes/cwl/02-1st-example. I've tr ...
written 9 months ago by karl.sebby70
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Comment: C: Is there a schema for CWL inputs/job files?
... Thanks! I remember coming across this at some point now... ...
written 11 months ago by karl.sebby70
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Comment: C: Is there a schema for CWL inputs/job files?
... Thanks. Will give it a try! ...
written 11 months ago by karl.sebby70
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Comment: C: bedtools sort -faidx in CWL
... If the command that you are trying to produce is `bedtools sort -header -faidx hg38.fasta.fai` it looks like you don't need `secondaryFiles` at all. You should just be able to pass in `hg38.fasta.fai` as your input file. ...
written 11 months ago by karl.sebby70
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Is there a schema for CWL inputs/job files?
... One thing I really like about CWL is the ability to load CWL files into a CommandLineTool or Workflow object after generating the classes using `schema-salad-tool --codegen=python CommonWorkflowLanguage.yml > cwl_classes.py`. Is there a schema file that describes CWL inputs/job files similar to C ...
cwl written 11 months ago by karl.sebby70
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Job: Python Software Engineer with Experience with Workflow Management, Whitefish, MT
... **xD Bio, Inc. https://xdbio.com, https://truwl.com** **Open Position:** Software Engineer **Job Description** xD Bio Inc. is seeking to expand our current small team with a motivated and experienced full stack software engineer with expertise in Python 3 and experience in bioinformatics and wo ...
python cwl job wdl written 13 months ago by karl.sebby70
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Comment: C: CWL: word counting
... Thanks for the example. Just what I needed right now. Was trying to use `stdin: $(inputs.text)` instead of `$(inputs.text.path)`. Also, interesting way to do a pipe using the arguments field instead of connecting `wc` and `awk` with a workflow. ...
written 2.4 years ago by karl.sebby70
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Comment: C: CWL: print out command lines?
... Hi sb10, Have you made any headway on this? I'm just circling back to this problem. ...
written 2.6 years ago by karl.sebby70

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