Summary

• Adds a -files-from option to nextflow lint that reads file paths from a file (one per line), avoiding the OS ARG_MAX limit when many files are passed as CLI arguments
• Supports reading from stdin via -files-from -
• Works additively with positional arguments — both sources are combined

Motivation

When using nextflow lint with tools like pre-commit on large repositories (1700+ .nf files), all filenames are passed as CLI arguments, which can exceed the OS ARG_MAX limit (~2MB on Linux), causing E2BIG: Argument list too long errors.

This is Option B from #6857 — a -files-from flag that reads file paths from a file, following the convention used by rsync, tar, and other Unix tools.

Usage

# Read paths from a file
nextflow lint -files-from filelist.txt

# Read paths from stdin
find . -name '*.nf' | nextflow lint -files-from -

# Combine with positional args
nextflow lint main.nf -files-from extra-files.txt

Changes

• CmdLint.groovy: Added -files-from parameter and file-reading logic in run() that reads lines, trims whitespace, skips blank lines, and appends paths to args before existing processing
• CmdLintTest.groovy: Added 3 tests — files-from basic usage, combined with positional args, and empty file list error handling

Testing

All 5 CmdLintTest tests pass (2 existing + 3 new).

Closes #6857