User: well309

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well30960
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Posts by well309

<prev • 6 results • page 1 of 1 • next >
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Answer: A: CWL rerunning completed output
... Hi Bruce, I also did not find any official documentation about caching system. I have been using CWL for processing dozens of genomic files with the cwl-runner software (https://github.com/common-workflow-language/cwltool). It has a working caching system. Here is how I run this software in product ...
written 7 weeks ago by well30960
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Answer: A: CWL bwa create index to bwa mem alignment workflow
... There are examples available at official repository (https://github.com/common-workflow-language/workflows). - BWA index: https://github.com/common-workflow-language/workflows/blob/master/tools/bwa-index.cwl - BWA mem: https://github.com/common-workflow-language/workflows/blob/master/tools/bwa-mem. ...
written 7 weeks ago by well30960
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CWL: Docker image as input parameter (for reference genome files)
... I am trying to figure out how can I copy reference genome files into Docker containers to be used by software aligners since CWL v1.0 does not support directory copy. One idea I am testing is to create a Docker image for the aligner itself and create a second image that derives `FROM` from the first ...
cwl written 3 months ago by well30960 • updated 16 days ago by Michael R. Crusoe690
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Comment: C: CWL: combine two arrays as workflow step input
... Thank you Michael. Here the code that worked. cwlVersion: v1.0 class: Workflow requirements: MultipleInputFeatureRequirement: {} inputs: files_1: File[] files_2: File[] outputs: task1_output: type: File outputSource: task1/outfile step ...
written 3 months ago by well30960
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Comment: C: CWL: combine two arrays as workflow step input
... Thank you Michael. I added a working example followed by the error message. Tool example (du): cwlVersion: v1.0 class: CommandLineTool baseCommand: [du] inputs: files: type: File[] inputBinding: {} outputs: outfile: type: stdout Workflow wit ...
written 3 months ago by well30960
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CWL: combine two arrays as workflow step input
... I'd like to know how can I combine two arrays (of string or File) into a single one in Common Workflow Language. For example: cwlVersion: v1.0 class: Workflow inputs: files_1: File[] files_2: File[] outputs: task1_output: type: File outputSource: ta ...
cwl written 3 months ago by well30960 • updated 3 months ago by Michael R. Crusoe690

Latest awards to well309

Scholar 4 weeks ago, created an answer that has been accepted. For A: CWL bwa create index to bwa mem alignment workflow

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