User: biokcb

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biokcb160
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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 4 months ago by biokcb160
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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 4 months ago by biokcb160
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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 4 months ago by biokcb160
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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 4 months ago by biokcb160 • updated 4 months ago by bogdan.gavrilovic170
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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 4 months ago by biokcb160
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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 4 months ago by biokcb160
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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 4 months ago by biokcb160 • updated 4 months ago by Michael R. Crusoe1.1k
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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 4 months ago by biokcb160
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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 5 months ago by biokcb160
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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 5 months ago by biokcb160

Latest awards to biokcb

Scholar 5 months ago, created an answer that has been accepted. For A: Staging subdirectories in CWL
Scholar 5 months ago, created an answer that has been accepted. For A: Staging subdirectories in CWL
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: String concatenation for output
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: String concatenation for output
Scholar 5 months ago, created an answer that has been accepted. For A: Staging subdirectories in CWL

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