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Fix #638 [MAG_DEPTHS_PLOT fails if only a single bin is produced] #639

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merged 10 commits into from
Aug 16, 2024
Merged

Fix #638 [MAG_DEPTHS_PLOT fails if only a single bin is produced] #639

merged 10 commits into from
Aug 16, 2024

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d-callan
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@d-callan d-callan commented Jul 18, 2024 •
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This PR fixes #638 by introducing a check against the number of rows in the bin depths files, and only attempting to produce heatmaps if there are > 2.

I'll work through the checklist shortly, though may need some guidance re testing (@jfy133 )

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 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).

@d-callan d-callan linked an issue Jul 18, 2024 that may be closed by this pull request
MAG_DEPTHS_PLOT fails if only a single bin is produced #638
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github-actions bot commented Jul 18, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 36cfd42

+| ✅ 307 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-15 19:33:53

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jfy133 commented Jul 22, 2024

@nf-core-bot fix linting

@d-callan
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d-callan commented Aug 9, 2024

so w some local testing i can confirm that :

  1. w this change we can now skip the MAG_DEPTHS_PLOT task and only that task
  2. my error has resolved and mag no longer fails for my test data
  3. any number of bins other than 1 does not cause failure

ive also updated changelog, etc. so i think maybe this is ready to be looked at..

@d-callan d-callan marked this pull request as ready for review August 9, 2024 17:53
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jfy133 commented Aug 10, 2024

@nf-core-bot fix linting

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jfy133 approved these changes Aug 15, 2024
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LGTM, sorry it took so long for such a small PR!

I'm going to add you to the contributors list and we are good to go :)

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jfy133 commented Aug 15, 2024

@nf-core-bot fix linting

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Appeasing linting...

subworkflows/local/depths.nf Outdated Show resolved Hide resolved
@jfy133 jfy133 merged commit 171ea0d into dev Aug 16, 2024
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@jfy133 jfy133 deleted the fix-638 branch August 16, 2024 07:36
@jfy133 jfy133 mentioned this pull request Aug 22, 2024
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MAG_DEPTHS_PLOT fails if only a single bin is produced
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