User: karl.sebby

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karl.sebby70
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Posts by karl.sebby

<prev • 17 results • page 1 of 2 • next >
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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 3 days 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 3 days 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 7 days 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 days ago by karl.sebby70 • updated 3 days ago by peter.amstutz300
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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 8 weeks 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 18 months 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 19 months ago by karl.sebby70
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Answer: A: CWL: print out command lines?
... OK. So I figured a few things out. If you are using the cwltool to run a job e.g. `$ cwltool echo.cwl echo.yml` where these files are echo.cwl cwlVersion: v1.0 class: CommandLineTool stdout: echoOutput.txt inputs: message: type: string inputBinding: ...
written 21 months ago by karl.sebby70
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Comment: C: CWL: print out command lines?
... I would like to know this as well. I'm digging through the cwltool code now to try and make it work. It shouldn't be too hard (famous last words) since the command is printed out when you run a job. It is not an option when running cwltool though. Will let you know if I figure it out. Hoping somebo ...
written 21 months ago by karl.sebby70
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Comment: C: Can I run ENCODE ChIP-Seq pipeline or get their code?
... The easiest solution would be to run it on DNAnexus platform. Or you could always try to get an account and see if you can see parameters there. I tried to get an account with my gmail address but was denied-- it wanted an institutional address so I'm not sure how hard it is to get onto their platfo ...
written 2.2 years ago by karl.sebby70

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