User: thomas.e

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thomas.e110
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Posts by thomas.e

<prev • 17 results • page 2 of 2 • next >
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cwl and resolution of enviroment variables
... Hello, I want to make CommandLineTool to wrap the platypus variant caller. Platypus expects to invoked as: python Platypus.py In other words, by default it doesn't have a handy wrapper script. Obviously, I could write one but I thought I ought to be handle a scenario like this in CWL as follow ...
cwl written 3.5 years ago by thomas.e110 • updated 3.4 years ago by wolfganggerlach198150
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Answer: A: cwl: how to add optional input as one element or as array of elements ?
... I used the solution here: https://www.biostars.org/p/218153/ ...
written 3.6 years ago by thomas.e110
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Comment: C: How process inputs based on a filename pattern using CWL
... Thanks, good suggestions. I'll look at option 2 - when (if) I get sufficiently proficient at CWL that even the smallest things don't take hours :) ...
written 3.6 years ago by thomas.e110
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How process inputs based on a filename pattern using CWL
... This must be answered somewhere but I can't find it. How do I process all files matching a pattern, e.g. /path/to/rawdata/*.dat I've seen examples where multiple inputs are explicitly listed but where a pattern is specified. ...
cwl written 3.6 years ago by thomas.e110
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Answer: A: CWL: default values for custom types in a workflow
... The answer is that I need to specify the type in the workflow input. i.e. inputs: mode: type: type.yml#end_mode default: PE ...
written 3.6 years ago by thomas.e110
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Answer: A: CWL: default values for custom types in a workflow
... I've made a minimal example that displays the problem. Here is the workflow: #!/usr/bin/env cwl-runner class: Workflow cwlVersion: v1.0 inputs: mode: type: string default: PE outputs: [] steps: echoecho: run: clt.cwl in: mode: mode out: [] Here is the command ...
written 3.6 years ago by thomas.e110
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CWL: default values for custom types in a workflow
... Hello, How do I set the default value for a custom type in a workflow. Something like: steps: mystep: run: mything.cwl in: important_arg: default: magicValue where `magic_value` is not a primitive type. In the example below it is an enum and ...
cwl written 3.6 years ago by thomas.e110 • updated 10 months ago by Biostar ♦♦ 20

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