User: karl.nordstrom

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Posts by karl.nordstrom

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Comment: C: CWL: How do I use pipes?
... you could make the inputs streamable as well. I'm not sure if stdout defaults to streamable. fileToSearch: type: File streamable: true inputBinding: position: 2 ...
written 3.7 years ago by karl.nordstrom90
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Answer: A: In CWL, how to make arrays optional input
... Setting type: string[]? makes it optional, but that only solves half the problem as it doesn't keep inputBinding perhaps: type: - null - type: array ... I havn't tested it though ...
written 3.7 years ago by karl.nordstrom90
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Comment: C: Directory or string type
... There are tool descriptions for some of the picard tools in the CWL repository: https://github.com/common-workflow-language/workflows/tree/master/tools Nothing with directory inputs though. I agree with StarvingMarvin's answer in general; Files and Directories for flexibility. Still, my experienc ...
written 3.8 years ago by karl.nordstrom90
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Answer: A: CWL: How do I use pipes?
... If you want to put it all together in a single CommandLineTool, you need to include ShellCommandRequirement. See: http://www.commonwl.org/v1.0/CommandLineTool.html#ShellCommandRequirement and for pipes and other interpreted characters you have to use shellQuote: False An alternative is to do a wo ...
written 3.8 years ago by karl.nordstrom90
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Comment: C: CWL: reading files within an expressionTool
... This solution works very well. I wasn't aware of the loadContent option. I aimed for something like processedoutput when I spoke of "set of arrays". Thank you very much. ...
written 3.9 years ago by karl.nordstrom90
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CWL: reading files within an expressionTool
... I am trying to convert a csv-file to a set of arrays with an expressionTool and have a piece of javascript that executes as intended when calling: node javaScript.js Due to lacking experience with java script I use googled solutions and when executing the script as a part of a cwl-pipeline it ...
common-workflow-language cwl javascript written 3.9 years ago by karl.nordstrom90 • updated 3.9 years ago by alaindomissy160
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Comment: C: Failing to use $mixin to include "global" settings
... OK, after doing some things wrong I found pull request 309 and it confirmed that I was on the right track :) I'll wait for it to resolve. It would be nice to have, but I can work around it for now. ...
written 3.9 years ago by karl.nordstrom90
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Comment: C: Failing to use $mixin to include "global" settings
... It might be that I'm duplicating this: https://github.com/common-workflow-language/common-workflow-language/pull/309 ...
written 3.9 years ago by karl.nordstrom90
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Comment: C: Failing to use $mixin to include "global" settings
... Thanks for the site. Very useful. Both files validate, but the tool helped me what could be the problem. The $mixin line is an entry in the inputs array. This leads to that the content of the settings.yml file becomes a subarray instead of being mixed in with the other elements. ...
written 3.9 years ago by karl.nordstrom90
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Answer: A: CWL Argument Error
... The problem is with the placement of the --debug flag The command should be: cwl-runner --debug bwa.cwl bwa.yml ...
written 3.9 years ago by karl.nordstrom90

Latest awards to karl.nordstrom

Popular Question 3.1 years ago, created a question with more than 1,000 views. For CWL: reading files within an expressionTool
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: CWL: How do I use pipes?

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