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Review of the MetaPhlAn4 #333

Merged
merged 10 commits into from
Jul 21, 2023
Merged

Review of the MetaPhlAn4 #333

merged 10 commits into from
Jul 21, 2023

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LilyAnderssonLee
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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/taxprofiler 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.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@LilyAnderssonLee
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@jfy133 Could you please change the MetaPhlAn3 into MetaPhlAn on the workflow chart within the file docs/output.md?

jfy133
jfy133 approved these changes Jul 20, 2023
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One tiny tweak and you're good to go :)

docs/usage.md Outdated Show resolved Hide resolved
@LilyAnderssonLee @jfy133
Update docs/usage.md
d2235ed 
Co-authored-by: James A. Fellows Yates <[email protected]>
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jfy133 commented Jul 20, 2023

Here are the files, you'll need to replace the ones in in docs/images with the following:

taxprofiler_tube
taxprofiler_tube.pdf
taxprofiler_tube

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jfy133 commented Jul 20, 2023 •
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Here are the 3 files (pdf, svg, png), you'll need to replace the ones in in docs/images with the following:

taxprofiler_tube
taxprofiler_tube.pdf
taxprofiler_tube

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github-actions bot commented Jul 20, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 087f293

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • 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 passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-21 10:47:40

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@jfy133 Apparently I need to modify the regular expression used within the MetaPhlAn4 module in order to run the MetaPhlAn3 database since these two versions of the database include different file formats.
Original code:

BT2_DB=`find -L "${metaphlan_db_latest}" -name "*rev.1.bt2l" -exec dirname {} \\;`
BT2_DB_INDEX=`find -L ${metaphlan_db_latest} -name "*.rev.1.bt2l" | sed 's/\\.rev.1.bt2l\$//' | sed 's/.*\\///'`

Modified version:

BT2_DB=`find -L "${metaphlan_db_latest}" -name "*rev.1.bt2*" -exec dirname {} \\;`
BT2_DB_INDEX=`find -L ${metaphlan_db_latest} -name "*.rev.1.bt2*" | sed 's/\\.rev.1.bt2.*\$//' | sed 's/.*\\///'`

I will create a PR to update the MetaPhlAn4 module if it's ok with you.

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jfy133 commented Jul 21, 2023

Yup sure!

@LilyAnderssonLee LilyAnderssonLee merged commit 47095d5 into nf-core:dev Jul 21, 2023
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@LilyAnderssonLee LilyAnderssonLee deleted the metaphlan4_profiler branch July 21, 2023 11:42
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@LilyAnderssonLee @jfy133