User: ionox0

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ionox0110
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Posts by ionox0

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Answer: A: InitialWorkDirRequirement error with array of Directories
... Answered my own question. It is the `listing` field that must evaluate to a list, so lists are not supported in the `entry` fields requirements: - class: InlineJavascriptRequirement - class: InitialWorkDirRequirement listing: $(inputs.directories) ...
written 14 days ago by ionox0110
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InitialWorkDirRequirement error with array of Directories
... I believe this should be supported as per the v1.0 spec cwlVersion: v1.0 class: CommandLineTool baseCommand: [touch] arguments: - ${return './' + inputs.directories[0].basename + '/' + inputs.to_touch} requirements: - class: InlineJavascriptRequirement - class: ...
cwl written 14 days ago by ionox0110
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Answer: A: Is there a good way to test CWL tools and workflows?
... Added as answer per @mr-c comment Some suggestions would be: 1. Testing with cwltool and the --js-console and --debug options. Also using --tmp-outdir-prefix, -leave-tmpdir, and --leave-outputs to inspect results from intermediate steps 2. Having small sample inputs that can be used to run the wo ...
written 14 days ago by ionox0110
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Comment: C: CWL: Setting output directories for steps in a workflow
... I have had the same question regarding CWL, and this is a helpful solution. I would be curious if there could eventually be a way to support referencing the files in the Directory class with a simple notation such as `my_directory.fastq_1`. There are several stages in our workflow that require r ...
written 14 days ago by ionox0110
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Comment: C: How to examine results files for a confirmation test
... Yes here is the documentation for `--leave-outptuts`: --leave-outputs Leave output files in intermediate output directories. ...
written 16 days ago by ionox0110
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CWL: Is there a way to have a list of imported Record types as an input?
... E.g. requirements: - $import: ../resources/schema_defs/fastq_pair.cwl inputs: fastq_pairs: type: type: array items: type: ../resources/schema_defs/fastq_pair.cwl#FastqPair ...
cwl written 5 weeks ago by ionox0110 • updated 24 days ago by Michael R. Crusoe970
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CWL: Is there a way to output an output file with one of the inputs of the tool in a Record type?
... I'm looking to do something like the following: cwlVersion: v1.0 class: CommandLineTool requirements: - class: InlineJavascriptRequirement - $import: Types.cwl ... inputs: an_input: string outputs: an_output: type: 'Types.cwl#Specia ...
cwl written 5 weeks ago by ionox0110 • updated 4 weeks ago by bogdan.gavrilovic110
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Comment: C: CWL: Is there a way to only pass certain fields from a `record` type to a step?
... Yes exactly, for the purpose of not having to list all the fields from the record type at each subworkflow layer of inputs ...
written 7 weeks ago by ionox0110
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Comment: C: More concise way to pass many parameters through to subworkflows
... It's just easier to group the parameters into one input so that you don't have to list them all in each inputs section. It's particularly cumbersome when there are several layers of subworkflows, and all you really want to do is just get the inputs to the underlying tool. I found that it is indeed ...
written 7 weeks ago by ionox0110
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Comment: C: Conflicting errors with "baseCommand" vs "arguments" usage
... Thank you fiakhan, yes my current solution is to supply large values for the `position` arguments, but I was wondering if there was a cleaner solution for that ...
written 9 weeks ago by ionox0110

Latest awards to ionox0

Teacher 12 days ago, created an answer with at least 3 up-votes. For A: InitialWorkDirRequirement error with array of Directories
Scholar 11 weeks ago, created an answer that has been accepted. For A: Taking directory path for reading as well as writing files
Scholar 11 weeks ago, created an answer that has been accepted. For A: What is the recommended way to debug JavaScript in CWL?
Scholar 4 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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