Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add an option to pass extra resources to vcfanno #588

Merged
merged 9 commits into from
Aug 9, 2024
Merged

Add an option to pass extra resources to vcfanno #588

merged 9 commits into from
Aug 9, 2024

Conversation

ramprasadn
Copy link
Collaborator

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/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>).
  • 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).

@github-actions GitHub Actions
Copy link

github-actions bot commented Aug 9, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 08302de

+| ✅ 186 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • 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
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-09 08:35:29

@ramprasadn ramprasadn marked this pull request as ready for review August 9, 2024 07:08
@ramprasadn ramprasadn requested review from jemten and rannick August 9, 2024 07:09
jemten
jemten reviewed Aug 9, 2024
View reviewed changes
Copy link
Collaborator

@jemten jemten left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Quick work Ram, some small comments

nextflow_schema.json Outdated Show resolved Hide resolved
subworkflows/local/annotate_mt_snvs.nf Outdated Show resolved Hide resolved
subworkflows/local/prepare_references.nf Outdated Show resolved Hide resolved
subworkflows/local/prepare_references.nf Outdated Show resolved Hide resolved
subworkflows/local/annotate_mt_snvs.nf Outdated
@@ -19,8 +19,9 @@ workflow ANNOTATE_MT_SNVS {
ch_cadd_header // channel: [mandatory] [ path(txt) ]
ch_cadd_resources // channel: [mandatory] [ path(annotation) ]
ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ]
ch_vcfanno_lua // channel: [mandatory] [ path(lua) ]
ch_vcfanno_resources // channel: [mandatory] [ path(resources) ]
ch_vcfanno_extra // channel: [mandatory] [ path(resources & indices) ]
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
ch_vcfanno_extra // channel: [mandatory] [ path(resources & indices) ]
ch_vcfanno_extra // channel: [mandatory] [ path(vcf), path(tbi) ]

Shouldn't it be something like this?

subworkflows/local/annotate_genome_snvs.nf Outdated
@@ -28,7 +28,8 @@ workflow ANNOTATE_GENOME_SNVS {
analysis_type // string: [mandatory] 'wgs' or 'wes'
ch_cadd_header // channel: [mandatory] [ path(txt) ]
ch_cadd_resources // channel: [mandatory] [ path(annotation) ]
ch_vcfanno_resources // channel: [mandatory] [ path(resources) ]
ch_vcfanno_extra // channel: [mandatory] [ path(resources & indices) ]
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
ch_vcfanno_extra // channel: [mandatory] [ path(resources & indices) ]
ch_vcfanno_extra // channel: [mandatory] [ path(vcf), path(tbi) ]

?

@ramprasadn ramprasadn requested a review from jemten August 9, 2024 08:21
jemten
jemten approved these changes Aug 9, 2024
View reviewed changes
Copy link
Collaborator

@jemten jemten left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

⭐

@ramprasadn ramprasadn merged commit fb9d2ef into dev Aug 9, 2024
6 checks passed
@jemten jemten deleted the dynamic-anno-res branch August 9, 2024 10:57
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jemten jemten jemten approved these changes

@rannick rannick Awaiting requested review from rannick

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@ramprasadn @jemten