Add support for comma-separated file paths in ProcessEntryHandler #6434
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- Add parseFileInput() helper method to handle comma-separated file paths - Support both String and GString inputs for file parameters - Return List<Path> for multiple files, single Path for one file - Handle whitespace trimming and empty string filtering - Maintain backward compatibility with existing single file behavior - Add comprehensive unit tests using Spock parameterized testing Usage: - Single file: --input file.txt (returns Path object) - Multiple files: --input "file1.txt,file2.txt,file3.txt" (returns List<Path>) - With whitespace: --input " file1.txt , file2.txt " (handles gracefully) 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
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Probably better to support space-separated files since it will usually be a glob pattern like |
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That can become tricky to handle file names with blanks |
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The same problem exists for a comma-separated list -- you have to quote or escape things either way |
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Nextflow CLI handles blank separated values as independent value. I mean if you have: a1.txt, a2.txt, and a3.txt and run:
instead, if you wrap in quotes:
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I see, so it's an issue with the CLI parsing. Should be something we can address in CLI v2 then |
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Yep |
bentsherman
reviewed
Sep 30, 2025
modules/nextflow/src/main/groovy/nextflow/script/ProcessEntryHandler.groovy
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bentsherman
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Sep 30, 2025
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Summary
Enhances ProcessEntryHandler to support comma-separated file paths for the
fileinput type, enabling users to pass multiple files in a single parameter.Changes
parseFileInput()helper method to handle comma-separated valuesList<Path>for multiple files, singlePathfor one fileUsage
🤖 Generated with Claude Code