User: biokcb

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biokcb150
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Posts by biokcb

<prev • 23 results • page 1 of 3 • next >
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Comment: C: CWL Workflow renaming outputs
... Will you add the `tar-param.cwl` script anyway so that we can figure out what you are referring to as having the same name? I think if you add it we can help you better. You can rename the output files, but I'm not 100% sure that's what you need in this case without seeing the command line tool. ...
written 9 weeks ago by biokcb150
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Comment: C: Capture Output files using glob
... I think you will need to go to the `inputs` section and change `$(inputs.splad_outDir)` from `type: Directory` to `type: string` for the script to set up a directory for you that does not exist. ...
written 10 weeks ago by biokcb150
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Comment: C: How to set default elements of a record?
... Thank you for the response! I am actually trying to avoid setting the default within the command line tool itself, but rather set defaults for a particular workflow so the tool can remain flexible for use in other workflows with different settings, it just needs the adapter path to be flexible. Woul ...
written 11 weeks ago by biokcb150
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How to set default elements of a record?
... Hi, I would like to create a workflow that sets default parameters for certain parts of a record and take input from the user for other parts. I want to keep the tool such that the inputs can be changed, but just set defaults for one particular workflow. I'm using the trimmomatic types found here: ...
cwl written 11 weeks ago by biokcb150 • updated 11 weeks ago by bogdan.gavrilovic150
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Comment: C: How does cwltool actually check file formats?
... Ok, it seems I just misunderstood this field. Thank you for the response! ...
written 11 weeks ago by biokcb150
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Comment: C: CWL passing secondary files in a workflow
... In your `degradation.cwl` script remove the `bai` entry under `inputs` ...
written 12 weeks ago by biokcb150
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How does cwltool actually check file formats?
... Hello! I am using a pre-made tool (trimmomatic) downloaded from https://github.com/common-workflow-language/workflows/tree/master/tools which has a file format specification (fastq). If I use an input file as such: input: class: File path: /path/to/myfile.fastq I get an error tha ...
cwl written 12 weeks ago by biokcb150 • updated 11 weeks ago by Michael R. Crusoe1.0k
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Comment: C: CWL passing secondary files in a workflow
... Try adding an initial work dir requirement index_bam.cwl (NOT Working code) cwlVersion: v1.0 class: CommandLineTool baseCommand: [samtools] doc: "samtools: index" requirements: InitialWorkDirRequirement: listing: [ $(inputs.bam) ] inputs: bam: ...
written 12 weeks ago by biokcb150
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Answer: A: CWL passing secondary files in a workflow
... It looks like part of the problem here is that you are trying to use an input `bai` that doesn't exist in your above `degradation.cwl` script. You could probably do one of two things: 1) Modify `degradation.cwl` to take the `.bai` file explicitly as input then use your `workflow.cwl` as is just by ...
written 12 weeks ago by biokcb150
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Comment: C: String editing for output file name
... Since `sample` is a `string` type, you don't need `basename`, as that is a File type attribute. Just use `glob: $(inputs.sample)_fastqc.summary` ...
written 3 months ago by biokcb150

Latest awards to biokcb

Scholar 3 months ago, created an answer that has been accepted. For A: Staging subdirectories in CWL
Scholar 3 months ago, created an answer that has been accepted. For A: Staging subdirectories in CWL
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: String concatenation for output
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: String concatenation for output
Scholar 3 months ago, created an answer that has been accepted. For A: Staging subdirectories in CWL

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