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fix macrel faa input #242

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merged 10 commits into from Apr 14, 2023
Merged

fix macrel faa input #242

merged 10 commits into from Apr 14, 2023

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Darcy220606
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@Darcy220606 Darcy220606 commented Mar 8, 2023 •
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This PR fixes the MACREL input issue in the pipeline amp workflow. The issue was that MACREL module is currently using fna and running its own annoations therfore when MACREl is run alone in the pipeline AMPCOMBI was not activated as it was missing one of its input = faa. To fix this i added the faa generated by MACREl into the summary channel. This closes issue #241
MACREL alse needs updating in FUNCSCAN/MODULES an issue #3001 was also created.

  • 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/funcscan branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
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  • 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).

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github-actions bot commented Mar 8, 2023 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6b34f55

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

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-04-13 17:17:17

@Darcy220606 Darcy220606 requested review from a team and removed request for jfy133, louperelo and jasmezz March 8, 2023 17:17
@Darcy220606 Darcy220606 linked an issue Mar 10, 2023 that may be closed by this pull request
AMPcombi does not execute when only MACREL #241
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louperelo
louperelo approved these changes Mar 15, 2023
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looks good to me
Took me a bit to understand how AMPcombi could deal with a channel if it contains two faa files, but realised it always considers the one on position 2 ...

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jfy133 commented Mar 17, 2023

@Darcy220606 please just check locally it works correctly now I've resolved the merge conflict, then you can merge :)

jfy133
jfy133 reviewed Mar 29, 2023
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louperelo
louperelo reviewed Apr 6, 2023
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Continues looking good.

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@Darcy220606 Darcy220606 merged commit 6c6ab7d into nf-core:dev Apr 14, 2023
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AMPcombi does not execute when only MACREL
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