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Tiddit pair VC #601

Merged
merged 21 commits into from
Jun 27, 2022
Merged

Tiddit pair VC #601

merged 21 commits into from
Jun 27, 2022

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WackerO
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@WackerO WackerO commented Jun 22, 2022

This PR enables TIDDIT for pair variant calling as a follow-up to #581 and #597

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).

@WackerO WackerO requested a review from maxulysse as a code owner June 22, 2022 12:42
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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @WackerO,

It looks like this pull-request is has been made against the WackerO/sarek master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the WackerO/sarek dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@WackerO WackerO changed the base branch from master to dev June 22, 2022 12:45
@WackerO

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github-actions bot commented Jun 23, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1475991

+| ✅ 145 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 2022-06-27 06:51:51

FriederikeHanssen
FriederikeHanssen reviewed Jun 24, 2022
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@FriederikeHanssen FriederikeHanssen left a comment

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Good work, some small comments left from my side

subworkflows/local/germline_variant_calling.nf Show resolved Hide resolved
subworkflows/local/pair_variant_calling.nf Show resolved Hide resolved
subworkflows/local/pair_variant_calling.nf Outdated Show resolved Hide resolved
subworkflows/local/pair_variant_calling.nf Show resolved Hide resolved
subworkflows/nf-core/variantcalling/svdb/main.nf Outdated Show resolved Hide resolved
conf/modules.config Show resolved Hide resolved
WackerO and others added 7 commits June 24, 2022 10:01
@WackerO @FriederikeHanssen
Update subworkflows/local/pair_variant_calling.nf
a1a634a 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
@WackerO @FriederikeHanssen
Update subworkflows/local/pair_variant_calling.nf
eee0ebb 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
@WackerO @FriederikeHanssen
Update subworkflows/local/pair_variant_calling.nf
5d3d00f 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
@WackerO
SVDB is published, removed unnecessary file, some cleanup
e6b0dcd
@WackerO
Merge branch 'dev' of https://github.com/nf-core/sarek into tidditpair
4225425
@WackerO
bugfix
31c55ae
@WackerO
linting
3f0c668
@FriederikeHanssen FriederikeHanssen merged commit 019fc68 into nf-core:dev Jun 27, 2022
@WackerO WackerO deleted the tidditpair branch July 27, 2022 09:01
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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