Ensure column ordering on get_mag_depths.py#911
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dialvarezs merged 3 commits intonf-core:devfrom Nov 4, 2025
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jfy133
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I can't really comment on the python code from a perspective of expertise, but I think I can follow - The 'main' line that fixes the bug is:
sample_names = sorted(sample_names)
right @dialvarezs ? This is what ensures consistent output ordering?
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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This PR address an issue I found when working on the snapshots.
In some (machine dependent?) cases, the
get_mag_depths.pywould not produce consistent column ordering on depth summaries, and as we are merging them the dummy way via.collectfile(keepHeader: true), that could result in partially swapped results in the final summary.Example of the outcome (same test, different machines):
I also improved the script a little to make it easier on the eyes.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).