Thanks to visit codestin.com
Credit goes to github.com

Skip to content

Patch Vitalstatistix #697

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
Merged
merged 30 commits into from
May 22, 2025
Merged

Patch Vitalstatistix #697

merged 30 commits into from
May 22, 2025

Conversation

@ramprasadn
Copy link
Collaborator

@ramprasadn ramprasadn commented Apr 22, 2025

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 pipelines 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
Copy link

github-actions bot commented Apr 22, 2025 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 608a2e6

+| ✅ 206 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  20 tests had warnings |!

❗ Test warnings:

  • local_component_structure - call_repeat_expansions.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - qc_bam.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - scatter_genome.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_mt_snvs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - call_structural_variants.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_structural_variants.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - rank_variants.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_repeat_expansions.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - gens.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - generate_cytosure_files.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_mobile_elements.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - call_snv.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - variant_evaluation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_references.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - subsample_mt.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - align.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_consequence_pli.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - generate_clinical_set.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_genome_snvs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - call_mobile_elements.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ 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 3.2.1
  • Run at 2025-05-22 09:42:37

jemten
jemten approved these changes Apr 24, 2025
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.

Looks good to me

@ramprasadn ramprasadn marked this pull request as ready for review April 24, 2025 07:42
Lucpen
Lucpen approved these changes Apr 24, 2025
View reviewed changes
Copy link
Contributor

@Lucpen Lucpen left a comment

Choose a reason for hiding this comment

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

LGTM!

ramprasadn and others added 24 commits April 29, 2025 12:41
@ramprasadn
concatenate calls
29e48af
@ramprasadn
update ci
91ce5e4
@ramprasadn
Update CHANGELOG.md
d354c05
@nf-core-bot
Template update for nf-core/tools version 3.2.1
aff6910
@ramprasadn
Merge remote-tracking branch 'origin/nf-core-template-merge-3.2.1' in…
eab8ca7 
…to patch
@ramprasadn
Merge branch 'patch' of github.com:nf-core/raredisease into patch
938330d
@ramprasadn
review suggestion
35358f8
@ramprasadn
Merge branch 'concat_mt_genome' of github.com:nf-core/raredisease int…
221b125 
…o concat_mt_genome
@ramprasadn
Merge branch 'patch' into concat_mt_genome
290a162
@ramprasadn
Merge pull request #699 from nf-core/concat_mt_genome
ffab51c 
concatenate nuclear and mt SNV calls
@ramprasadn
lint
76f155a
@ramprasadn
update version
b60aab2
@ramprasadn
update link
a516f0f
@ramprasadn
add verifybamid
2ed8a9e
@ramprasadn
update module with stub
d4055b2
@ramprasadn
update metromaps
4300637
@ramprasadn
update docs & add module to multiqc report
b03d134
@ramprasadn
updatae changelog
bbbbf6e
@ramprasadn
review suggestions
a6f08a6
@ramprasadn
fix lint
11b3d73
@ramprasadn
update parameter name
793fe48
@ramprasadn
add citations
cb97ec0
@ramprasadn
Merge pull request #701 from nf-core/verifybamid2
0ca26c1 
Add Verifybamid2
@ramprasadn
add mitochondria-mode arg to filtermutect2
537e71e
@ramprasadn ramprasadn merged commit 46afe31 into master May 22, 2025
16 checks passed
@ramprasadn ramprasadn deleted the patch branch June 25, 2025 08:53
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

@Lucpen Lucpen Lucpen approved these changes

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

5 participants

@ramprasadn @jemten @Lucpen @nf-core-bot