User: bogdan.gavrilovic

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Posts by bogdan.gavrilovic

<prev • 17 results • page 1 of 2 • next >
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Comment: C: CWL join two dimensional file array output
... Did you consider using StepInputExpressionRequirement (https://www.commonwl.org/v1.0/Workflow.html#StepInputExpressionRequirement)? You can set a `valueFrom` using JS expression and transform a step input with $(self[0]) from, e.g. [ [ 1, 2 ] ] to [ 1, 2 ]. ...
written 9 weeks ago by bogdan.gavrilovic210
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Answer: A: Load/parse cwl in python
... You can use `pyyaml`. Install with `pip install pyyaml` Load a CWL (which can be in JSON or YAML format) using with open(cwl_file_path, 'r') as cwl_file: cwl_dict = yaml.safe_load(cwl_file) This will return a python dict with all the fields. ...
written 8 months ago by bogdan.gavrilovic210
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Answer: A: best practice for renaming file in CWL workflow
... I would suggest adding a simple `mv` command to the end of the command line, via arguments, e.g. ``` arguments: - position: 1000 shellQuote: false valueFrom: ' && mv $(inputs.fastq1.basename) $(inputs.add_rg_SM)_R1.fastq.gz' ``` then you could just glob `$(inputs.add ...
written 9 months ago by bogdan.gavrilovic210
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Comment: C: scatter over optional argument
... Yes, that is correct. ...
written 9 months ago by bogdan.gavrilovic210
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Answer: A: Rules regarding secondaryFiles in subworkflows
... This depends on where you run the workflow. Some executors have a feature to delete unnecessary intermediate files to save up on disk space during execution. Setting the secondary file on output of the first step would signal that the `^.bai` file is needed and should not be deleted. ...
written 11 months ago by bogdan.gavrilovic210
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Answer: A: scatter over optional argument
... Hi, There's two issues here. 1) Looks like the input for the step (workflow input) was not a list, but null(not defined). The scatter method must work with a list on input. At least an empty list should be provided `[ ]`. 2) If you scatter over an empty list, 0 commands will be execute ...
written 11 months ago by bogdan.gavrilovic210
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Answer: A: How to set default elements of a record?
... I suppose that you want to add this parameter to the command line somewhere. You can use `arguments` to add the desired default value if the original value is not set. inputs: - id: window type: type: record fields: - name: windowSize ...
written 12 months ago by bogdan.gavrilovic210
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Answer: A: Is there a way to convert ["null", File] to File in CWL?
... Hi, I think you have no reason for concern. When an input/output type is defined as any list of types, e.g. `[string, File]` - it means that the item that appears on that input/output in execution is one of these possible types (unless input is a defined as `[wave, particle]`, in that case it ca ...
written 13 months ago by bogdan.gavrilovic210
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Answer: A: Input type array and Output type file, possible in CWL ?
... Hi, seems to me like you are doing everything right regarding CWL. Possible problem could be that when you scatter `fastqc_check.cwl`, two jobs are created and each job outputs the file with the same name `$(inputs.sample)_fastqc.summary`. Try to change the `fastqc_check.cwl` tool to output some ...
written 13 months ago by bogdan.gavrilovic210
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Answer: A: Reading Array from File as Input at Runtime
... The modified expression tool would look like this. ``` cwlVersion: v1.0 class: ExpressionTool requirements: { InlineJavascriptRequirement: {} } inputs: a_File: type: File inputBinding: loadContents: true expression: | ${ return { "array_string": JSON.parse(inputs.a_File.content ...
written 13 months ago by bogdan.gavrilovic210

Latest awards to bogdan.gavrilovic

Scholar 8 months ago, created an answer that has been accepted. For A: Use filename found in an input Directory in a CommandLineTool
Scholar 11 months ago, created an answer that has been accepted. For A: Use filename found in an input Directory in a CommandLineTool
Scholar 13 months ago, created an answer that has been accepted. For A: Use filename found in an input Directory in a CommandLineTool
Scholar 13 months ago, created an answer that has been accepted. For A: Use filename found in an input Directory in a CommandLineTool
Scholar 15 months ago, created an answer that has been accepted. For A: Use filename found in an input Directory in a CommandLineTool
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Use filename found in an input Directory in a CommandLineTool
Scholar 15 months ago, created an answer that has been accepted. For A: Use filename found in an input Directory in a CommandLineTool
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Use filename found in an input Directory in a CommandLineTool

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