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Vep update #482

Merged
merged 11 commits into from
Jan 22, 2024
Merged

Vep update #482

merged 11 commits into from
Jan 22, 2024

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ramprasadn
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PR checklist

Addresses #477

  • 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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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).

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github-actions bot commented Jan 16, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f1b75d4

+| ✅ 155 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowRaredisease.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • 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: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-22 14:09:42

@ramprasadn ramprasadn marked this pull request as ready for review January 16, 2024 19:52
@ramprasadn ramprasadn requested a review from jemten January 22, 2024 09:16
jemten
jemten reviewed Jan 22, 2024
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Nice! Some minor comments.

conf/test.config Show resolved Hide resolved
conf/test_one_sample.config
@@ -58,10 +58,5 @@ params {
vep_cache = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz"
vep_filters = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt"
vep_cache_version = 107
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110?

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Same here

nextflow_schema.json
@@ -383,6 +383,15 @@
"help_text": "If no directory path is passed, vcf files will not be annotated by vep.",
"fa_icon": "fas fa-folder-open"
},
"vep_plugin_files": {
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could you add a specific schema for this input. Mainly checking that the files exists.

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also, don't you need to add this file to option to nextflow.config?

nextflow_schema.json Outdated
"description": "Databases used by both named and custom plugins to annotate variants.",
"fa_icon": "fas fa-file-csv",
"help_text": "Path to a file containing the absolute paths to databases and their indices used by VEP's custom and named plugins resources defined within the vcfanno toml file. One line per resource.",
"mimetype": "text/csv"
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could you add a pattern arrument to ensure .csv file ending

subworkflows/local/annotate_genome_snvs.nf Outdated Show resolved Hide resolved
subworkflows/local/annotate_mobile_elements.nf Outdated Show resolved Hide resolved
subworkflows/local/annotate_mt_snvs.nf Outdated Show resolved Hide resolved
ramprasadn and others added 2 commits January 22, 2024 15:04
@ramprasadn
review suggestions
1b1d6a1
@ramprasadn @jemten
Apply suggestions from code review
f1b75d4 
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
jemten
jemten approved these changes Jan 22, 2024
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👍

@jemten jemten merged commit c397a04 into nf-core:dev Jan 22, 2024
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@jemten jemten deleted the vep_update branch January 22, 2024 15:23
@jemten jemten mentioned this pull request Jan 24, 2024
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@ramprasadn @jemten