User: ionox0

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ionox0330
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Posts by ionox0

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Comment: C: Why is ShellCommandRequirement necessary for Pipes
... Glad it's helpful! It is also helpful for myself to be able to explain it. Another thing I realized was that even though the command is printed like that by cwltool when it runs the command, cwltool is a python process, and it's not the same as running the command from a shell / terminal outside CWL ...
written 4 weeks ago by ionox0330
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Comment: C: Why is ShellCommandRequirement necessary for Pipes
... Thanks Tom! I still don't understand whether additiona arguments need to be quoted after the pipe when using `/bin/sh -c`, or whether that doesn't matter. ...
written 4 weeks ago by ionox0330
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Answer: A: Why is ShellCommandRequirement necessary for Pipes
... Answered my own question after a bit of research: `ShellCommandRequirement` in CWL allows us to use `/bin/sh -c` in order to pass our command as a string to a shell intrepreter. `ShellQuote:false` leaves shell metacharacters unquoted, and thus they can still be interpreted and used by a shell. Fr ...
written 4 weeks ago by ionox0330
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Why is ShellCommandRequirement necessary for Pipes
... This is a general question regarding the `ShellCommandRequirement` feature. Would anyone happen to be able to explain why `ShellCommandRequirement` is required to use Pipes in the CWL arguments section? The pipes will work if I use `ShellCommandRequirement` and set `ShellQuote` to `false` for the ...
cwl written 4 weeks ago by ionox0330
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Comment: C: Upgrade to 3.18 no longer allows optional parameters to be omitted
... Sorry, to be clear that tool is Toil ...
written 8 weeks ago by ionox0330
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Answer: A: Upgrade to 3.18 no longer allows optional parameters to be omitted
... Update: I have found that this error is dependent on the `tool.cwl` having a default for the optional parameter. I've included a minimal reproducible example here: https://github.com/DataBiosphere/toil/issues/2512 I believe it is related to the combination of a subworkflow with an optional tool p ...
written 8 weeks ago by ionox0330
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Upgrade to Toil 3.18 no longer allows optional parameters to be omitted when passed through subworkflow
... I've upgraded from 3.15 to 3.18 and found that previously it was possible to have an optional argument, that when left blank by the parent workflow, would run the CommandLineTool with the argument supplied as `null`: inputs: fci__basq_fix: string? ... steps: run: tool.cwl ...
toil cwl written 8 weeks ago by ionox0330
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Answer: A: Creating a temporary directory for tools to use
... Thank you to @Mr-C for the answer to this one: A variation on http://www.commonwl.org/user_guide/14-runtime/index.html is at https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/writable-dir-docker.cwl class: CommandLineTool requirements: - ...
written 3 months ago by ionox0330
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Creating a temporary directory for tools to use
... What would be the easiest way to make a directory using CWL? For example a temporary directory that needed to exist for a tool to run ...
cwl written 3 months ago by ionox0330
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Comment: C: How to specify enum symbols in record type definition?
... Thank you for the help and improvements! ...
written 3 months ago by ionox0330

Latest awards to ionox0

Scholar 3 months ago, created an answer that has been accepted. For A: CWL: array of files as an input
Scholar 3 months ago, created an answer that has been accepted. For A: CWL: array of files as an input
Scholar 4 months ago, created an answer that has been accepted. For A: CWL: array of files as an input
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: toil stats under-reporting memory usage?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: InitialWorkDirRequirement error with array of Directories
Supporter 5 months ago, voted at least 25 times.
Popular Question 6 months ago, created a question with more than 1,000 views. For What is the recommended way to debug JavaScript in CWL?
Scholar 8 months ago, created an answer that has been accepted. For A: CWL: array of files as an input
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: InitialWorkDirRequirement error with array of Directories
Scholar 11 months ago, created an answer that has been accepted. For A: Taking directory path for reading as well as writing files
Scholar 11 months ago, created an answer that has been accepted. For A: What is the recommended way to debug JavaScript in CWL?
Scholar 13 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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