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Tiddit subworkflow #651

Merged
merged 12 commits into from
Jul 19, 2022
Merged

Tiddit subworkflow #651

merged 12 commits into from
Jul 19, 2022

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WackerO
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@WackerO WackerO commented Jul 18, 2022 •
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This PR extracts tiddit from pair VC into a separate subworkflow

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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/sarek 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).
  • 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).

@FriederikeHanssen
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This superseded #637 then, right?

@WackerO
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WackerO commented Jul 18, 2022 •
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This superseded #637 then, right?

I would suggest first merging #637 and then merging this PR separately, I am working on two different branches for the two things

@FriederikeHanssen
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but you are including tabix in both?

@WackerO
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WackerO commented Jul 18, 2022

Well yes, #637 introduces it and 651 moves it together with the rest of TIDDIT. Or should the indexing still be done in pairVC, not in the new tiddit subworkflow?

@FriederikeHanssen
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well but if you remove tabix and add it once the mulled container is there in #651 then we can merge this on e now-ish.

@WackerO
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WackerO commented Jul 19, 2022

On it. Took me a bit to find out how what I needed to change in the modules.config. I hope all the tests run...

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github-actions bot commented Jul 19, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7b252d9

+| ✅ 146 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-19 12:07:02

WackerO and others added 3 commits July 19, 2022 13:11
@WackerO @FriederikeHanssen
Update conf/modules.config
45953be 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
@WackerO
Still bugfixing
e840cdb
@WackerO
Should work now(?)
7b252d9
@WackerO
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WackerO commented Jul 19, 2022

fiiinally tiddit seems to work. I had to re-enable the vcf,vcf.gz though (from your last review) or the pytest would throw errors...

@WackerO WackerO marked this pull request as ready for review July 19, 2022 12:30
@WackerO WackerO requested a review from maxulysse as a code owner July 19, 2022 12:30
@WackerO WackerO merged commit d840af4 into nf-core:dev Jul 19, 2022
@WackerO WackerO deleted the tiddit_sw branch July 27, 2022 09:00
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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@WackerO @FriederikeHanssen