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Fix null in depth PNG files #522

Merged
merged 1 commit into from
Oct 7, 2023
Merged

Fix null in depth PNG files #522

merged 1 commit into from
Oct 7, 2023

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jfy133
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@jfy133 jfy133 commented Oct 6, 2023 •
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Replaces #521 I got confused and thought that the bins going into depths were technically separated by domain - but that is not the case.

closes #518

IN this case you essentially want to aggregate by sample/assembler/binner and display all these within the heatmap. The Tiara/domain info at this stage just acts as an indicator which bins are more likely eukarotyic, which is ireelevant for the depth heatmaps.

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>).
  • Usage Documentation in docs/usage.md is updated.
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github-actions bot commented Oct 6, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d511ebd

+| ✅ 158 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   3 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowMag.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-06 12:48:35

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Also LGTM, assuming you've tested it 😁

@jfy133
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jfy133 commented Oct 7, 2023

I think it makes sense now 😬, and yes tested

@jfy133 jfy133 merged commit 04e2b57 into dev Oct 7, 2023
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@jfy133 jfy133 deleted the fix-null-in-depths branch October 7, 2023 08:49
@jfy133 jfy133 mentioned this pull request Oct 9, 2023
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@prototaxites prototaxites prototaxites approved these changes

@d4straub d4straub Awaiting requested review from d4straub

@CarsonJM CarsonJM Awaiting requested review from CarsonJM

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