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

Adapt vcf to scout #127

Merged
merged 11 commits into from
May 28, 2024
Merged

Adapt vcf to scout #127

merged 11 commits into from
May 28, 2024

Conversation

Lucpen
Copy link
Collaborator

@Lucpen Lucpen commented May 27, 2024

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
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,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 May 27, 2024 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 843579f

+| ✅ 159 tests passed       |+
#| ❔ 317 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: 2.0.1
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-28 06:32:57

This was linked to issues May 27, 2024
vcfs with only one variant per line so that they can be handled by Scout #125
Closed
Add tag in vcf #126
Closed
@Lucpen Lucpen marked this pull request as ready for review May 27, 2024 08:26
@Lucpen Lucpen requested a review from a team as a code owner May 27, 2024 08:26
@Lucpen Lucpen added bug Something isn't working enhancement New feature or request labels May 27, 2024
Lucpen
Lucpen commented May 27, 2024
View reviewed changes
CHANGELOG.md Outdated Show resolved Hide resolved
Lucpen
Lucpen commented May 27, 2024
View reviewed changes
CHANGELOG.md Show resolved Hide resolved
jemten
jemten reviewed May 27, 2024
View reviewed changes
Copy link
Contributor

@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.

Nice work lucia! It would be good to also make sure that the vcfs coming from the call_variants sub workflow is normalised and decomposed.

subworkflows/local/allele_specific_calling.nf Outdated
Comment on lines 114 to 131
ch_genome_chrsizes.flatten().map{chromsizes ->
return [[id:variant_caller], chromsizes]
}
.set { ch_varcallerinfo }

ADD_VARCALLER_TO_BED (ch_varcallerinfo).gz_tbi
.map{meta,bed,tbi -> return [bed, tbi]}
.set{ch_varcallerbed}

REMOVE_DUPLICATES.out.vcf
.join(TABIX_REMOVE_DUP.out.tbi)
.combine(ch_varcallerbed)
.combine(ch_foundin_header)
.set { ch_annotate_in }

BCFTOOLS_ANNOTATE(ch_annotate_in)

TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf)
Copy link
Contributor

Choose a reason for hiding this comment

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

I would move this to the call_variants subworkflow.

Copy link
Collaborator Author

Choose a reason for hiding this comment

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

Done!

subworkflows/local/allele_specific_calling.nf Outdated Show resolved Hide resolved
subworkflows/local/allele_specific_calling.nf Outdated Show resolved Hide resolved
conf/modules/allele_specific_calling.config Show resolved Hide resolved
conf/modules/allele_specific_calling.config Outdated Show resolved Hide resolved
jemten
jemten reviewed May 27, 2024
View reviewed changes
conf/modules/allele_specific_calling.config Outdated
Comment on lines 52 to 58
withName: '.*ALLELE_SPECIFIC_CALLING:ADD_VARCALLER_TO_BED' {
ext.args2 = '-s 1 -b 2 -e 3'
}

withName: '.*ALLELE_SPECIFIC_CALLING:BCFTOOLS_ANNOTATE' {
ext.args = "-c CHROM,FROM,TO,FOUND_IN --output-type z"
ext.prefix = { "${meta.id}_split_rmdup_info" }
Copy link
Contributor

Choose a reason for hiding this comment

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

Let's remove this part since we now add the variant caller in the call_variants subworkflow

Copy link
Collaborator Author

Choose a reason for hiding this comment

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

Done!

jemten
jemten approved these changes May 28, 2024
View reviewed changes
Copy link
Contributor

@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.

🎉

@Lucpen Lucpen merged commit e68af17 into dev May 28, 2024
6 checks passed
@Lucpen Lucpen deleted the adapt_vcf_2_scout branch May 28, 2024 06:50
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

Assignees
No one assigned
Labels
bug Something isn't working enhancement New feature or request
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Add tag in vcf vcfs with only one variant per line so that they can be handled by Scout
2 participants
@Lucpen @jemten