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Snapshot for -profile test_assembly_input#905

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dialvarezs merged 24 commits intonf-core:devfrom
dialvarezs:snapshot_assembly_input
Nov 12, 2025
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Snapshot for -profile test_assembly_input#905
dialvarezs merged 24 commits intonf-core:devfrom
dialvarezs:snapshot_assembly_input

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@dialvarezs dialvarezs commented Oct 28, 2025

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).

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dialvarezs commented Oct 30, 2025

@nf-core-bot fix linting

@dialvarezs dialvarezs changed the title Snapshot for test_assembly_input Snapshot for -profile test_assembly_input Oct 30, 2025
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dialvarezs commented Oct 31, 2025 •
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Ok, after a long time struggling this the stability of this snapshot, it's finally ready for merging.

The instability because of:

  • An issue of the publishing of BUSCO files, it's fixed now
  • Inconsistent sorting on CSV files. I added a sort step in the Python scripts to keep bin_summary.tsv stable.

Regarding BUSCO, I found out that is not able to produce consistently sorted CSV batch files, even when running with a single core... So I decided to left out of the snapshots both *.batch_summary.txt and busco_summary.tsv.

@dialvarezs dialvarezs marked this pull request as ready for review October 31, 2025 19:18
@dialvarezs dialvarezs linked an issue Oct 31, 2025 that may be closed by this pull request
Generate snapshot for test_assembly_input #900
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dialvarezs commented Nov 3, 2025

I also updated the get_mag_depths.py script to produce depth summaries with consistent column ordering, to prevent swapped depth values on the merged depth summary.

d4straub
d4straub reviewed Nov 4, 2025
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I got a few questions, but generally I think the PR is great, and it uncovered already some bugs, thats what its for! :)

Comment thread conf/modules.config Outdated
Comment thread conf/modules.config Outdated
Comment thread conf/test_assembly_input.config Outdated
Comment thread conf/test_assembly_input.config Outdated
Comment thread tests/test_assembly_input.nf.test
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dialvarezs commented Nov 12, 2025 •
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I added some basic CSV checks for busco_summary and bin_summary files. I also updated the nft-utils plugin.
And fixed the error reporting of tiara_classify that was breaking the test_alternatives test.

Most of the small fixes I did on this PR originally were ported to other PR for v5.2.0, so this PR has become more simple now.

prototaxites
prototaxites approved these changes Nov 12, 2025
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A few questions/comments, but this is looking fine as-is!

Comment thread tests/test_alternatives.nf.test
Comment thread tests/test_assembly_input.nf.test
Comment thread tests/test_assembly_input.nf.test
@dialvarezs dialvarezs merged commit 5868522 into nf-core:dev Nov 12, 2025
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@dialvarezs dialvarezs mentioned this pull request Dec 1, 2025
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@d4straub d4straub d4straub left review comments

@prototaxites prototaxites prototaxites approved these changes

@jfy133 jfy133 Awaiting requested review from jfy133 jfy133 is a code owner

@muabnezor muabnezor Awaiting requested review from muabnezor muabnezor is a code owner

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Generate snapshot for test_assembly_input

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