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Implementation of lofreq somatic and callparallel to sarek as variant callers #1602

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wants to merge 21 commits into from
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Implementation of lofreq somatic and callparallel to sarek as variant callers #1602

wants to merge 21 commits into from

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AitorPeseta
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@AitorPeseta AitorPeseta commented Jul 24, 2024 •
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#1588

  • 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 (nf-test test tests/ --verbose --profile +docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

We wanted to ask you for a code review in this PR. We are updating Sarek with new modules: lofreq somatic (paired sample variant calling) and lofreq callparallel (tumor-only variant calling). Therefore, there will be two new subworkflows: one for somatic and the other one for tumor-only.

In order to these modules fitting in Sarek, we have made some changes in them in this fork. Consequently, they are not exactly the same modules from nf-core modules repo (they will be updated when we finish this). For this reason, we will be working in parallel to update these modules in nf-core/modules.

To sum up, we wanted to ask for a code review, specifically in these new lofreq subworkflows.

@AitorPeseta AitorPeseta added the enhancement New feature or request label Jul 24, 2024
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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 @AitorPeseta,

It looks like this pull-request is has been made against the AitorPeseta/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 AitorPeseta/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!

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github-actions bot commented Jul 24, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 3e445d0

+| ✅ 200 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   3 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • 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: .gitignore or .prettierignore
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-08 10:32:04

@AitorPeseta AitorPeseta changed the base branch from master to dev July 24, 2024 09:51
@nevinwu
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nevinwu commented Aug 1, 2024

We have implemented lofreq call-parallel as a variant caller for sarek. We have included bedtools sort and bedtools merge in a intervals.bed processing step to ensure the bed file is properly formed. If it is not, lofreq raises an error. Please let us know if we should keep or remove this bed-processing step.

Unfortunately, we weren't able to implement lofreq somatic due to the way this software works. It generates several "intermediate" files and, if one of these doesn't have somatic variants (which is indeed pretty possible as we've checked with targetseq panel data) lofreq raises and error. Consequently, nextflow stops its execution.

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nevinwu commented Aug 7, 2024

@nf-core-bot fix linting

@AitorPeseta
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@nf-core-bot fix linting

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nevinwu commented Aug 8, 2024

@nf-core-bot fix linting pretty please

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AitorPeseta commented Aug 9, 2024 •
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@nevinwu and I have decided to close this PR and make the same changes in the Dev branch instead of the master, as it seems that Prettier has changed many files, and that was not our intention.

@AitorPeseta AitorPeseta closed this Aug 9, 2024
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@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

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

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@nevinwu nevinwu

@AitorPeseta AitorPeseta

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