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Fix combine #464

Merged
merged 6 commits into from
Apr 7, 2024
Merged

Fix combine #464

merged 6 commits into from
Apr 7, 2024

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Midnighter
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@Midnighter Midnighter commented Mar 27, 2024 •
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Fix #460, bug in combining Kaiju and mOTUs profiles with their respective databases.

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!
  • CHANGELOG.md is updated.

@Midnighter Midnighter self-assigned this Mar 27, 2024
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github-actions bot commented Mar 27, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 399b87c

+| ✅ 193 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-07 00:53:22

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One more commit with a larger refactoring incoming, but I want to see if 5858a42 passes the tests first.

@Midnighter Midnighter marked this pull request as draft March 27, 2024 16:42
@Midnighter Midnighter marked this pull request as ready for review March 27, 2024 16:59
@Midnighter Midnighter linked an issue Mar 27, 2024 that may be closed by this pull request
Failed to produce kaiju_combined_reports.txt #460
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Getting this error often now that you also described @LilyAnderssonLee.

ERROR ~ Cannot invoke method split() on null object

 -- Check script './workflows/../subworkflows/local/profiling.nf' at line: 152 or see '.nextflow.log' file for more details

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After several restarts, tests are passing successfully.

jfy133
jfy133 approved these changes Mar 28, 2024
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@LilyAnderssonLee is doing the proper review, but a brief skim conceptually looks good to me

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jfy133 commented Mar 28, 2024

I should have fixed the split() error in #461 now

LilyAnderssonLee
LilyAnderssonLee approved these changes Apr 6, 2024
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Well done!

subworkflows/local/standardisation_profiles.nf Outdated Show resolved Hide resolved
subworkflows/local/standardisation_profiles.nf Outdated Show resolved Hide resolved
@Midnighter Midnighter merged commit a9afbc0 into dev Apr 7, 2024
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@Midnighter Midnighter deleted the fix-combine branch April 7, 2024 08:21
@LilyAnderssonLee LilyAnderssonLee mentioned this pull request Apr 8, 2024
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@LilyAnderssonLee LilyAnderssonLee LilyAnderssonLee approved these changes

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Failed to produce kaiju_combined_reports.txt
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@Midnighter @jfy133 @LilyAnderssonLee