User: grange

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grange0
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Posts by grange

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Comment: C: [cwl] referencing to list of paths in an array of files or direcories
... Answering my own question. Curious to see if this is indeed the neatest option: class: CommandLineTool cwlVersion: v1.0 baseCommand: - python inputs: - id: inpfiles inputBinding: position: 0 type: 'Directory[]' outputs: [] lab ...
written 2.0 years ago by grange0
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Answer: A: [cwl] referencing to list of paths in an array of files or direcories
... Actually, the issue now is that the variable that is passed contains a lot of data (including the list of files for each directory) which causes python to bail out with an OSError due to the argument list being too long. Any hints on keeping the data that is put on the command line short? I am using ...
written 2.0 years ago by grange0
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Answer: A: [cwl] referencing to list of paths in an array of files or direcories
... Works like a charm! Thanks! ...
written 2.0 years ago by grange0
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[cwl] referencing to list of paths in an array of files or direcories
... I try to refer to a list of input paths in a CommandLineTool. In essence, my tool looks like this: class: CommandLineTool cwlVersion: v1.0 baseCommand: - python inputs: - id: inpfiles type: 'Directory[]' outputs: [] label: _do_magic argumen ...
cwl written 2.0 years ago by grange0
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Gather sorting by parameter in the metadata of input file
... In our processing, we'd like to gather the results of one CommandLineTool that is running in parallel, making groups of a predefined size (say: group every 6 files) and grouped by a meta data value from the data (say: frequency). What would be the most CWLy way to achieve this? Does the language s ...
cwl gather written 2.2 years ago by grange0 • updated 2.2 years ago by Michael R. Crusoe1.8k

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