nf-core / nf-core/nft-utils

Function to recursively check all detected files for a specific string

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#23 2 comments 0 reactions 1 assignee View on GitHub

@tom-seqera is already working on this.

Since Oct 29, 2024.

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Java
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Description

Currently there are two helper methods for checking output files:

  • Find all files with a pattern and generate an md5 (when contents stable between tests)
  • Find all files with a pattern and check existence by file name (when contents are unstable between tests)

While the of unstability fallback is good e.g. binary files, it's not as good as checking inside a file for consistent contents (E.g. when maybe it's only a single timestamp inside the file is unstable).

An intermediate check is to check for certain strings, e.g. maybe 'SUCCESSFUL RUN' at the end of a log.

It would be nice to have a function that does the same as the two existing methods, but with the string checking functionality.

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