User: eduardo

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eduardo0
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Posts by eduardo

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CWL 'glob' field not capturing files
... In my workflow, I am unable to capture specific files using the 'glob' field from one of the step that outputs an array of files. The glob is ignored and I end up with all files. I have tried the following: outputs: sss_out: # type: File doesn't work. It has to be a file arra ...
cwl written 6 days ago by eduardo0 • updated 6 days ago by Michael R. Crusoe750
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Comment: C: Filter array of files to one file
... valueFrom: $( self.filter(file => !!file.basename.match(/^.*\.ids\.txt$/)).pop() ) ...
written 9 days ago by eduardo0
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Comment: C: Filter array of files to one file
... I tried to acknowledge https://www.biostars.org/u/15908/, but I didn't found a way to link to a specific gitter message. Or were referring to this other post? https://www.biostars.org/p/282785/ I made another post because https://www.biostars.org/p/282785/ was about converting a file to string. The ...
written 9 days ago by eduardo0
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Answer: A: Filter array of files to one file
... Add an ExpressionTool step to filter: cwlVersion: v1.0 class: ExpressionTool requirements: { InlineJavascriptRequirement: {} } inputs: files: type: File[] expression: | ${ return {"ids": inputs.files.filter(file => !!file.basename.match(/^.*\.ids\.txt ...
written 9 days ago by eduardo0
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Answer: A: Filter array of files to one file
... Michael R. Crusoe point out a couple of solutions: At workflow level: in: single_file: source: other_step/array_of_files valueFrom: $(self[0]) ...
written 9 days ago by eduardo0
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Filter array of files to one file
... One step in my workflow produces File[] and I need to filter to grab just one File for the next step. I am trying to use glob without much success. Any hints? ...
cwl written 9 days ago by eduardo0
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Comment: C: Converting stdout (File) to string
... This solution also has the 64kb limitation, correct? ...
written 13 days ago by eduardo0
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Comment: C: Converting stdout (File) to string
... Thanks! That's what I was looking for. ...
written 13 days ago by eduardo0
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Comment: C: Converting stdout (File) to string
... Output from first step: outputs: accessions: type: stdout Input from second step: inputs: sequences: type: string ...
written 13 days ago by eduardo0
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Converting stdout (File) to string
... I am constructing a workflow that contains two steps: 1. the output of the first step is stdout (compatible, I believe, with File type) 2. the input of the second is a string I am not able to modify these steps. How can I connect these two steps? Do I have to make an adaptor step? ...
cwl written 13 days ago by eduardo0 • updated 12 days ago by Michael R. Crusoe750

Latest awards to eduardo

Scholar 9 days ago, created an answer that has been accepted. For A: Filter array of files to one file
Scholar 9 days ago, created an answer that has been accepted. For A: Filter array of files to one file

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