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fix: gzipped files on METABINNER_BINS to prevent race condition#1058

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dialvarezs wants to merge 3 commits into
nf-core:devfrom
dialvarezs:feat/metabinner-improvements
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fix: gzipped files on METABINNER_BINS to prevent race condition#1058
dialvarezs wants to merge 3 commits into
nf-core:devfrom
dialvarezs:feat/metabinner-improvements

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@dialvarezs

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When running MetaBinner on our HPC (storage mounted via NFS), I got the following error:

find: ./bins/.nfs000000100122bb1600001c93: No such file or directory

This happens because when find starts, the file is still visible in the NFS filesystem, but by the time the mv command runs, the file has already been unlinked, throwing an error.
This chamge makes the script generating the bin files gzipped, so the post-execution of gzip and mv is no longer required.

This also changes the boundary of too short bins (< to <=) to align with what the tool does.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@dialvarezs dialvarezs self-assigned this Jun 25, 2026
@dialvarezs dialvarezs changed the title fix: emit gzipped files on METABINNER_BINS for race condition fix: emit gzipped files on METABINNER_BINS / race condition Jun 25, 2026
@dialvarezs dialvarezs changed the title fix: emit gzipped files on METABINNER_BINS / race condition fix: gzipped files on METABINNER_BINS to prevent race condition Jun 25, 2026
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