Fix get_wf_files to use git ls-files#4068
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jonasscheid wants to merge 2 commits intonf-core:devfrom
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….gitignore parsing
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Description
get_wf_files()usesfnmatchto filter files based on.gitignorepatterns, butfnmatchdoes not implement gitignore semantics correctly. For example, a.gitignoreentrywork/should matchscripts/work/at any depth, butfnmatch.fnmatch("scripts/work/file", "work/*")returnsFalse. This causespipeline_if_empty_null(the only caller) to walk and open every file in untracked directories — freezing indefinitely on pipelines with large Nextflow work directories.Replace the manual
.gitignoreparsing +fnmatchapproach withgit ls-files, which natively respects all.gitignorerules. This matches the existingPipeline.list_files()method that already uses this approach.