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Fix: Correct vep_cache_path_full when refseq/merged option is present #1563

Merged
merged 3 commits into from
Jun 12, 2024
Merged

Fix: Correct vep_cache_path_full when refseq/merged option is present #1563

merged 3 commits into from
Jun 12, 2024

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YeHW
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@YeHW YeHW commented Jun 12, 2024

In this PR, I'm trying to fix this issue: ensembl-vep refseq/merged option broken.

Let's assume these param values:

vep_cache: path/to/vep_cache_dir
vep_cache_version: "111"
vep_genome: GRCh37
vep_species: homo_sapiens
vep_custom_args: "--everything --format vcf"

As of sarek 3.4.2, we can feed custom VEP options via params.vep_custom_args to the pipeline.

If --refseq or --merged is in params.vep_custom_args, it will be passed to VEP's final command, and result in the following effects:

  • If --refseq is provided, VEP will use ${vep_cache}/${vep_species}_refseq/${vep_cache_version}_${vep_genome} as the annotation source
  • If --merged is provided, VEP will use ${vep_cache}/${vep_species}_merged/${vep_cache_version}_${vep_genome} as the annotation source

Reference: https://useast.ensembl.org/info/docs/tools/vep/script/vep_options.html

When this happens (Let's assume --refseq is in params.vep_custom_args), in the ANNOTATION_CACHE_INITIALISATION workflow, a wrong vep_cache_path_full path will be tested if exists, because it won't check if params.vep_custom_args contains --refseq.

I modified the related code such that in the ANNOTATION_CACHE_INITIALISATION workflow, vep_cache_path_full will be built correctly by taking into consideration if --refseq or --merged is present in params.vep_custom_args.

I've tested with in-house data, and it worked as expected: when --refseq is present, VCF files will be annotated with RefSeq cache (e.g. "homo_sapiens_refseq/111_GRCh37"); when neither --refseq nor --merged is present, they will be annotated with normal cache (e.g. "homo_sapiens/111_GRCh37).

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 (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.
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  • README.md is updated (including new tool citations and authors/contributors).

@YeHW YeHW self-assigned this Jun 12, 2024
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github-actions bot commented Jun 12, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c051a5e

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

❗ 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 2024-06-12 09:37:59

@YeHW
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YeHW commented Jun 12, 2024 •
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I changed the signature of ANNOTATION_CACHE_INITIALISATION workflow, resulting this error (which is expected because I passed an additional parameter params.vep_custom_args to it)

ERROR ~ Workflow `NFCORE_SAREK:ANNOTATION_CACHE_INITIALISATION` declares 10 input channels but 11 were given

If adding a new parameter to this workflow is ok, I guess we need to change the declarations to 11?
@maxulysse

Nevermind, I forget one line of code.

@maxulysse maxulysse merged commit ff9a474 into nf-core:dev Jun 12, 2024
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@YeHW YeHW mentioned this pull request Jun 12, 2024
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@maxulysse maxulysse maxulysse approved these changes

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

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