User: ionox0

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ionox0370
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Posts by ionox0

<prev • 63 results • page 1 of 7 • next >
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Comment: C: interesting behavior with grep
... Thanks for the tip, I didn't consider using this feature, indeed the `successCodes` feature solves this problem more cleanly. The result of the cwl is the following: $ /bin/sh \ -c \ 'head' '-n' '1' '/scratch/tmpeZmeI2/stg3e5bd4d3-f4b3-40c3-be05-689bb0bcd8cf/Sample_1_Annotated_Evidenc ...
written 7 weeks ago by ionox0370
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interesting behavior with grep
... This isn't a question as much as an interesting finding, to get `grep` to work with the `-v` flag when the entire file is grepped-out, you need to add `|| true` to make sure the jobs doesn't fail due to a nonzero exit code from grep. For example this tool concatenates several vcf files together, bu ...
cwl written 8 weeks ago by ionox0370
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Difference between TMPDIR environment variable, --workdir in Toil / CWL
... I was wondering whether anyone could explain the difference between the TMPDIR environment variable that is used by cwltool and the --workDir parameter that is used by Toil. Which is used for what purpose, and will one override the other when using Toil 3.15? If this question could use some additi ...
toil cwl written 3 months ago by ionox0370
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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 5 months ago by ionox0370
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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 5 months ago by ionox0370
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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 5 months ago by ionox0370
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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 5 months ago by ionox0370
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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 6 months ago by ionox0370
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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 6 months ago by ionox0370
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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 6 months ago by ionox0370

Latest awards to ionox0

Scholar 7 months ago, created an answer that has been accepted. For A: CWL: array of files as an input
Scholar 8 months ago, created an answer that has been accepted. For A: CWL: array of files as an input
Scholar 9 months ago, created an answer that has been accepted. For A: CWL: array of files as an input
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: toil stats under-reporting memory usage?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: InitialWorkDirRequirement error with array of Directories
Supporter 10 months ago, voted at least 25 times.
Popular Question 10 months ago, created a question with more than 1,000 views. For What is the recommended way to debug JavaScript in CWL?
Scholar 12 months ago, created an answer that has been accepted. For A: CWL: array of files as an input
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: InitialWorkDirRequirement error with array of Directories
Scholar 16 months ago, created an answer that has been accepted. For A: Taking directory path for reading as well as writing files
Scholar 16 months ago, created an answer that has been accepted. For A: What is the recommended way to debug JavaScript in CWL?
Scholar 17 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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