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Merged
maxulysse merged 19 commits into from
Nov 11, 2024
Merged

Add deepsomatic module scaffolding #6622

maxulysse merged 19 commits into from
Nov 11, 2024
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@vaxyzek
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@vaxyzek vaxyzek commented Sep 10, 2024 •
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This is a first version of PR to add deepsomatic capabilities into nf-core/modules.

PR checklist

Closes #XXX

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test deepsomatic --profile docker

@vaxyzek vaxyzek requested review from a team and mashehu and removed request for a team September 10, 2024 17:04
@vaxyzek vaxyzek marked this pull request as draft September 10, 2024 17:05
@maxulysse maxulysse mentioned this pull request Sep 12, 2024
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maxulysse commented Sep 12, 2024

@nf-core-bot fix linting pretty please 🙏

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github-actions bot commented Sep 12, 2024

Nothing for me to do here! 🤷
This is probably because the linting errors come from nf-core lint and have to be fixed manually (or with nf-core lint --fix).

maxulysse
maxulysse reviewed Sep 12, 2024
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maxulysse
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@vaxyzek vaxyzek requested a review from maxulysse October 23, 2024 20:20
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maxulysse commented Nov 1, 2024

@nf-core-bot fix linting pretty please 🙏

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maxulysse commented Nov 1, 2024

Please @nf-core-bot fix linting pretty please 🙏 🙏

maxulysse
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vaxyzek commented Nov 5, 2024

hi @maxulysse, I've committed proposed input channels re-arrangement and excluded deepsomatic from conda and singularity tests.

sateeshperi
sateeshperi reviewed Nov 6, 2024
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modules/nf-core/deepsomatic/tests/main.nf.test
{ assert process.success },
{
assert snapshot(
process.out.vcf.collect { file(it[1]).getName() },
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can you try using the nft-vcf plugin to see if you can get an md5 ?

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If I remember well the VCF is empty, so not super useful here.
I'll play around that in Sarek

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maxulysse commented Nov 11, 2024

@nf-core-bot fix linting pretty please 🙏

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github-actions bot commented Nov 11, 2024

Nothing for me to do here! 🤷
This is probably because the linting errors come from nf-core lint and have to be fixed manually (or with nf-core lint --fix).

maxulysse
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maxulysse reviewed Nov 11, 2024
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@maxulysse maxulysse marked this pull request as ready for review November 11, 2024 17:21
@maxulysse maxulysse requested review from a team and mirpedrol November 11, 2024 17:21
@maxulysse maxulysse enabled auto-merge November 11, 2024 17:22
@maxulysse maxulysse disabled auto-merge November 11, 2024 17:28
@maxulysse maxulysse added this pull request to the merge queue Nov 11, 2024
Merged via the queue into nf-core:master with commit 89e06f6 Nov 11, 2024
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@maxulysse maxulysse maxulysse approved these changes

@sateeshperi sateeshperi sateeshperi left review comments

@mashehu mashehu Awaiting requested review from mashehu

@mirpedrol mirpedrol Awaiting requested review from mirpedrol

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@vaxyzek @maxulysse @sateeshperi @nf-core-bot