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Fix input to single-end MEGAHIT runs #729

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merged 2 commits into from
Dec 14, 2024
Merged

Fix input to single-end MEGAHIT runs #729

merged 2 commits into from
Dec 14, 2024

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jfy133
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@jfy133 jfy133 commented Dec 10, 2024

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).

jfy133
jfy133 commented Dec 10, 2024
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jfy133 commented Dec 10, 2024

Closes #727

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github-actions bot commented Dec 10, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3020a1c

+| ✅ 323 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 3.0.2
  • Run at 2024-12-10 12:06:45

sateeshperi
sateeshperi requested changes Dec 10, 2024
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fix tests

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jfy133 commented Dec 11, 2024

Uh-oh....

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jfy133 commented Dec 11, 2024

Replicated failure and this is the error:

(nf-core) james@bionb103:~/git/nf-core/mag/testing/work/17/c9f0a089e501713e8d3ba4fd0b5846 (fix-megahit)$ cat MEGAHIT-MetaBAT2-test_minigut.1.fa_busco.err
2024-12-11 17:04:42 ERROR:      list_of_reference_markers.bacteria_odb10.txt is not a valid option for 'placement_files'
2024-12-11 17:04:42 ERROR:      BUSCO analysis failed!
2024-12-11 17:04:42 ERROR:      Check the logs, read the user guide (https://busco.ezlab.org/busco_userguide.html), and check the BUSCO issue board on https://gitlab.com/ezlab/busco/issues

@jfy133 jfy133 requested a review from sateeshperi December 13, 2024 15:17
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jfy133 commented Dec 13, 2024

@sateeshperi the BUSCO database is working now :D

@sateeshperi sateeshperi merged commit 7aebfa8 into dev Dec 14, 2024
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@sateeshperi sateeshperi deleted the fix-megahit branch December 14, 2024 02:55
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