Add known_hash file() option

[edmundmiller]

Overview

This PR adds a new file hash verification feature to Nextflow's file() operator. This feature allows users to verify file integrity by checking file hashes against expected values. This feature is particularly useful when working with downloaded files or when ensuring data integrity is critical.

Implementation Details

• Added FileHashVerifier class that supports multiple hash algorithms:
  • MD5
  • SHA-1
  • SHA-256
  • SHA-384
  • SHA-512
• Extended the file() operator to accept a known_hash parameter in the format algorithm:hash
• Added comprehensive test coverage in FileHashVerifierTest
• Updated documentation in working-with-files.md

Usage Example

// Verify a file with MD5
file('data.txt', known_hash: 'md5:d41d8cd98f00b204e9800998ecf8427e')
// Verify a file with SHA-256
file('data.txt', known_hash: 'sha256:e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855')

Limitations

• Hash verification is not supported when using glob patterns that match multiple files

• Throws an IllegalArgumentException if:

  • Hash format is invalid
  • Hash algorithm is not supported
  • File hash doesn't match the expected value

  Inspiration

This feature was inspired by the Pooch library, which provides similar functionality for Python.

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[bentsherman]

I think Jordi took a crack at this a few years ago: #4415

I guess now we have two approaches we can compare 😅

[pditommaso]

Suggested change

	file('some/path/to/my_file.file', known_hash: 'md5:d41d8cd98f00b204e9800998ecf8427e')
	file('some/path/to/my_file.file', checksum: 'md5:d41d8cd98f00b204e9800998ecf8427e')

checksum may be preferable

[bentsherman]

I think I like Jordi's approach better. The problem with this PR is that it verifies the checksum when you call file(), but file() should only give you a reference, it should not trigger a download.

@edmundmiller would you be willing to test Jordi's PR and build on it instead? If you can confirm that it works then that will make it easier to merge