User: ionox0

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ionox0280
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Posts by ionox0

<prev • 51 results • page 1 of 6 • next >
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Comment: C: How to specify enum symbols in record type definition?
... Thank you for the help and improvements! ...
written 1 day ago by ionox0280
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How to specify enum symbols in record type definition?
... I like to use `SchemaDefRequirements` to define parameter groups for our tools. Is it possible to include the symbols field under the record fields that have type `enum`? Thank you! name: vcf2maf_params type: record fields: species: type: enum? # This doesn't pass ...
cwl written 20 days ago by ionox0280 • updated 12 days ago by Michael R. Crusoe1.1k
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Comment: C: best practice for renaming file in CWL workflow
... Yes, this looks like a good solution, and is perhaps better practice than modifying the `basename` of the output itself I also wonder if a new cwl step entirely would be an even more robust / cleaner solution ...
written 20 days ago by ionox0280
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Answer: A: CWL pipe doesn't seem to be working
... Ah, silly me, I can see that I included the `Requirements` section twice. I assume the second one overwrote the first and killed the `ShellCommandRequirement`. ...
written 23 days ago by ionox0280
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CWL pipe doesn't seem to be working (Solved: user error)
... For some reason when I run the following command in the terminal it works (VCF file comes out with proper header as given by the `var2vcf_paired.pl` script). However in the cwl workflow this command appears to only run everything before the first pipe, and the two subsequent steps aren't run. Is the ...
cwl written 23 days ago by ionox0280
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Comment: C: best practice for renaming file in CWL workflow
... Thank you! The following syntax works: processed_fastq_1: type: File outputBinding: glob: $('*/' + inputs.fastq1.basename) outputEval: | ${ self[0].basename = inputs.add_rg_SM + '_R1.fastq.gz'; return self[0] ...
written 6 weeks ago by ionox0280
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Comment: C: best practice for renaming file in CWL workflow
... Thanks very much @mr-c! My suggestion for changing the output file name would be something like: outputs: out_thing: glob: *.fastq newName: my_new_name.fastq If I have time I could put more research into how to implement this feature. ...
written 6 weeks ago by ionox0280
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Answer: A: size considerations CWL Toil workflow step inputs
... I found that the inputs to this step add up to 236GB (pretty close to 234GB from the warning), so it seems like they are indeed being considered for the `diskMinRequirement` ...
written 7 weeks ago by ionox0280
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size considerations CWL Toil workflow step inputs
... I'm experiencing a disk usage warning using Toil with CWL: w01.cbio.private 2018-10-17 04:22:20,803 Thread-403 WARNING toil.statsAndLogging: Got message from job at time 10-17-2018 04:22:20: Job used more disk than requested. Consider modifying the user script to avoid the chance of failure due ...
toil cwl written 7 weeks ago by ionox0280
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Comment: C: toil stats under-reporting memory usage?
... https://github.com/DataBiosphere/toil/pull/2425 ...
written 7 weeks ago by ionox0280

Latest awards to ionox0

Scholar 20 days ago, created an answer that has been accepted. For A: CWL: array of files as an input
Scholar 7 weeks ago, created an answer that has been accepted. For A: CWL: array of files as an input
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: toil stats under-reporting memory usage?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: InitialWorkDirRequirement error with array of Directories
Supporter 11 weeks ago, voted at least 25 times.
Popular Question 3 months ago, created a question with more than 1,000 views. For What is the recommended way to debug JavaScript in CWL?
Scholar 5 months ago, created an answer that has been accepted. For A: CWL: array of files as an input
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: InitialWorkDirRequirement error with array of Directories
Scholar 8 months ago, created an answer that has been accepted. For A: Taking directory path for reading as well as writing files
Scholar 8 months ago, created an answer that has been accepted. For A: What is the recommended way to debug JavaScript in CWL?
Scholar 10 months ago, created an answer that has been accepted. For A: Taking directory path for reading as well as writing files

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