User: ionox0

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ionox0120
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Posts by ionox0

<prev • 31 results • page 1 of 4 • next >
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Comment: C: scatter over optional argument
... Thank you @bogdan! Would it also work with multiple elements in the list? As in would the `--illumina` value get applied to multiple jobs if `adapters: [null]`? Or will it only process the first pair of fastqs? ...
written 13 days ago by ionox0120
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Rules regarding secondaryFiles in subworkflows
... I have workflow a step that outputs the following: outputs: standard_bams: type: File[] outputSource: flatten_array_bams/output_bams and a subsequent step that accepts this^ output: inputs: standard_bam: type: File secondaryFiles: [^.bai] I was ...
cwl written 19 days ago by ionox0120 • updated 13 days ago by bogdan.gavrilovic150
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Comment: C: scatter over optional argument
... No it's not an output from a previous step ...
written 5 weeks ago by ionox0120
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Comment: C: scatter over optional argument
... I want to be able to provide an array of adapter sequences to scatter over (`string[]: [adapter1, adapter2, ...]`), but if the adapters are not provided I would like to be able to provide another argument to the tool to specify it to use the default illumina adapter (`string: --illumina`), in which ...
written 5 weeks ago by ionox0120
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scatter over optional argument
... Is it possible to scatter over an optional argument (of type `string[]?`) when the argument isn’t provided? The message that I get from cwltool when trying this is: [workflow standard_bam_generation] starting step module_1 Unhandled exception Traceback (most recent call last): F ...
cwl written 6 weeks ago by ionox0120 • updated 13 days ago by bogdan.gavrilovic150
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Answer: A: Is there a way to set a basename for an output Directory?
... I got this to work with the following example: clipping_dir: type: Directory outputBinding: glob: '*/' outputEval: | ${ self[0].basename = inputs.fastq1.basename.split('_R1_')[0] + '_umi_clipping_results'; return sel ...
written 6 weeks ago by ionox0120
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Is there a way to set a basename for an output Directory?
... For example: clipping_dir: type: Directory outputBinding: glob: '*/' outputEval: | ${ self.basename = inputs.fastq1.basename.replace('_R1_*', ''); return self } This results in the following output direc ...
cwl written 7 weeks ago by ionox0120
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Answer: A: InitialWorkDirRequirement copies or symlinks files?
... Thank you @mr-c for the answer, which is also in the CWL spec: If writable is false, the file may be made available using a bind mount or file system link to avoid unnecessary copying of the input file. ...
written 7 weeks ago by ionox0120
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InitialWorkDirRequirement copies or symlinks files?
... For InitialWorkDirRequirement, do the files get copied to the current directory or symlinked? It seems that they are symlinked. The reason that I have this question is because I would like to use `glob: .` and reference these InitialWorkDir files in a later step. However it seems that the the link ...
cwl written 8 weeks ago by ionox0120
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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 11 weeks ago by ionox0120

Latest awards to ionox0

Scholar 6 weeks ago, created an answer that has been accepted. For A: CWL: array of files as an input
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: InitialWorkDirRequirement error with array of Directories
Scholar 4 months ago, created an answer that has been accepted. For A: Taking directory path for reading as well as writing files
Scholar 4 months ago, created an answer that has been accepted. For A: What is the recommended way to debug JavaScript in CWL?
Scholar 6 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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