User: liuxf09

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liuxf0930
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Posts by liuxf09

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Answer: A: secondaryFiles for bam: how to handle .bai or/and ^.bai ?
... One solution is extend the spec of cwl to add an attribute "optional" to secondaryFiles items, like secondaryFiles: - .bai optional: true - .^bai optional: true This will make secondaryFiles mechanism more flexible. ...
written 2.9 years ago by liuxf0930
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Comment: C: secondaryFiles for bam: how to handle .bai or/and ^.bai ?
... As a workflow, I would like to get the flow to work with both .bam.bai and .bai index files. To make a more symbolic link from .bai to .bam.bai is a workaround. ...
written 2.9 years ago by liuxf0930
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secondaryFiles for bam: how to handle .bai or/and ^.bai ?
... Bam file could have two different file extensions depending on the tools. Given bam file test.bam, - test.bam.bai secondaryFiles = [.bai] - test.bai secondaryFiles = [^.bai] For a flow to work with both kinds of bam inputs, how to set the secondaryFiles? Since secondaryFiles items must ...
cwl written 2.9 years ago by liuxf0930
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Answer: A: how to make seconaryFiles work for File in CommandInputRecordField
... One ticket is filed on github/cwltool ( https://github.com/common-workflow-language/cwltool/issues/480 ). ...
written 3.0 years ago by liuxf0930
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Answer: A: how to make seconaryFiles work for File in CommandInputRecordField
... If it is going to support `secondaryFiles` in `InputRecordField`, the fix is straight foward: In `schemas/v1.0/Process.yml`, there is a `secondaryFiles` field under `Parameter`. Just copy this field to under InputRecordField after label field. ...
written 3.0 years ago by liuxf0930
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Answer: A: how to make seconaryFiles work for File in CommandInputRecordField
... My another question is: Is the support of `seconaryFiles` in `CommandInputRecordField` general enough? Should this be added to cwl standard? ...
written 3.0 years ago by liuxf0930
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how to make seconaryFiles work for File in CommandInputRecordField
... I have a input parameter that is an array of records, like the following: resources: type: type: array items: - type: record name: resource fields: - name: resource type: File inputBinding: ...
cwl written 3.0 years ago by liuxf0930
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Comment: C: cwl: how to add optional input as one element or as array of elements ?
... I tried the hack to use `itemSeparator`. But the command line created has quote for items connected by itemSeparator, which causes error in option parsing in the binary. It is common in my application to mix usage of single input or multiple inputs like `--opt input1 --opt input 2`. Is it a good id ...
written 3.0 years ago by liuxf0930
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Comment: C: cwl: how to add optional input as one element or as array of elements ?
... Hi, Bioinformatics_NewComer: I think I don't understand what you meant. Can you give some code example? Thanks ...
written 3.0 years ago by liuxf0930
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cwl: how to add optional input as one element or as array of elements ?
... I often need support optional input as File or as array of File entries. For example, I want to create command line option like the following: `--opt A --opt B --opt C` I can define the following in cwl: inputs: opt: type: - "null" - type: array i ...
cwl written 3.1 years ago by liuxf0930 • updated 3.0 years ago by thomas.e110

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