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Add full size test NA12878#604

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ggabernet merged 7 commits intonf-core:devfrom
ggabernet:full-tests
Jun 30, 2022
Merged

Add full size test NA12878#604
ggabernet merged 7 commits intonf-core:devfrom
ggabernet:full-tests

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@ggabernet ggabernet commented Jun 24, 2022

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/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 --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).

@ggabernet ggabernet marked this pull request as ready for review June 24, 2022 07:43
@ggabernet ggabernet requested a review from maxulysse as a code owner June 24, 2022 07:43
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github-actions Bot commented Jun 24, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit bc4bebe

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ 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 2022-06-28 08:15:42

maxulysse
maxulysse reviewed Jun 24, 2022
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Comment thread conf/test_full.config Outdated
FriederikeHanssen
FriederikeHanssen reviewed Jun 24, 2022
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Comment thread conf/test_full.config Outdated
FriederikeHanssen
FriederikeHanssen reviewed Jun 27, 2022
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Comment thread conf/test_full.config Outdated

// Other params
tools = 'strelka,freebayes,haplotypecaller,vep'
tools = 'strelka,freebayes,haplotypecaller,deepvariant,manta,tiddit,ascat,snpeff,vep'
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@FriederikeHanssen FriederikeHanssen Jun 27, 2022

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ASCAT only works for paired samples at the moment., cnvkit however is also implemented for germline only mode

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@maxulysse maxulysse Jun 27, 2022

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Do we really want to do annotation? The containers are huge

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@ggabernet ggabernet Jun 28, 2022

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well it's a full test so it shouldn't matter much, but maybe just VEP for now then

@ggabernet ggabernet merged commit 105d5ad into nf-core:dev Jun 30, 2022
@FriederikeHanssen FriederikeHanssen mentioned this pull request Jul 1, 2022
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@maxulysse maxulysse maxulysse approved these changes

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@ggabernet @maxulysse @FriederikeHanssen
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