Skip to content

feat: Add cnv report generation - #147

Open
fevac wants to merge 11 commits into
devfrom
add_cnv_report
Open

feat: Add cnv report generation#147
fevac wants to merge 11 commits into
devfrom
add_cnv_report

Conversation

@fevac

@fevac fevac commented Jun 23, 2026 •
edited by kristinebilgrav
Loading

Copy link
Copy Markdown
Collaborator

Closes: https://github.com/Clinical-Genomics/MTP-oncoflow/issues/34

This feature includes:

@fevac
feat: Add parameters for cnv report (#104)
1daaeab 
Part of Clinical-Genomics/MTP-oncoflow#34

### Added

- Parameters for cnv report: cnv_gene_tsv, cnv_segment_tsv
@github-actions

github-actions Bot commented Jun 23, 2026

Copy link
Copy Markdown

PR checklist

  • Fill in description of the PR and link to any relevant issues.
  • If you've fixed a bug, added a subworkflow or any other code that should be tested, add tests!
  • If you've added a new tool, update citations according to the instructions under Adding Citations.
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • README.md is updated (including authors/contributors).

See Contributing Guidelines for more details on how to contribute according to pipeline conventions.

@fevac
feat: Add markdown script for CNV report generation (#89)
9f5187e 
This script is part of
Clinical-Genomics/MTP-oncoflow#34

### Added

- Markdown script for CNV report generation, that takes two CNV tables
(at gene and segment level) and creates a interactive report where those
tables are searchable and sortable.
@fevac fevac changed the title feat: Add cnv report generation (#104) feat: Add cnv report generation Jun 23, 2026
kristinebilgrav and others added 9 commits June 24, 2026 11:20
@kristinebilgrav
merge dev
f2b058b
@kristinebilgrav
feat: update test dataset path to include CNV files (#151)
a5fc25d 
A part of: Clinical-Genomics/MTP-oncoflow#34

### Changed

- Updated the `pipelines_testdata_base_path` to include the latest
commit with CNV test files
@kristinebilgrav
update documentation
7ebfe86
@kristinebilgrav
merge dev
f13143d
@kristinebilgrav
remove files
6fed205
@kristinebilgrav
fix schema
7c45a1a
@fevac @kristinebilgrav
feat: add nf-core rmarkdownotebook module and PROCESS_CNVS subwor…
0038355 
…kflow for CNV report generation (#126)

Part of: Clinical-Genomics/MTP-oncoflow#34

### Added

- nf-core rmarkdownotebook module
- PROCESS_CNV subworkflow with CNV report generation step
    - subworkflow test and snapshot for process_cnvs

### Changed

- Updated tests with files for the subworkflow
    - the cnv report will be ignored from the tests
- Updated snapshots for pipeline tests

---------

Co-authored-by: kristinebilgrav <kristinebilgrav1@gmail.com>
Co-authored-by: Kristine Bilgrav <77359122+kristinebilgrav@users.noreply.github.com>
@kristinebilgrav
merge dev
f1b4d63
@kristinebilgrav
merge dev
684fb44
@github-actions

github-actions Bot commented Aug 3, 2026

Copy link
Copy Markdown

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

@github-actions

github-actions Bot commented Aug 3, 2026

Copy link
Copy Markdown

nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 684fb44

+| ✅ 191 tests passed       |+
#| ❔  21 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  13 tests had warnings |!
-| ❌   1 tests failed       |-
Details

❌ Test failures:

  • modules_json - Your modules.json file is outdated. It will be automatically generated by running any module command.

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • 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.
  • 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
  • schema_lint - Schema 'description' should be 'Customizable post-processing and extension layer for Oncoanalyser that adapts its outputs according to clinical and operational needs, adds missing analyses, and ensures flexibility for evolving standards while retaining Oncoanalyser's robust core.'
    Found: 'Customizable post-processing and extension layer for Oncoanalyser that adapts its outputs according to clinical and operational needs, adds missing analyses, and ensures flexibility for evolving standards while retaining Oncoanalyser's robust core.'
  • schema_lint - Parameter input not found in schema

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.3
  • Run at 2026-08-03 12:02:05

@github-actions

github-actions Bot commented Aug 3, 2026

Copy link
Copy Markdown

❌ nf-test failed with latest Nextflow version

Note

Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing.

  • ❌ docker | latest-everything | Shard 2/7

See the full run for details.

@kristinebilgrav
kristinebilgrav marked this pull request as ready for review August 3, 2026 12:19
@kristinebilgrav
kristinebilgrav requested a review from a team as a code owner August 3, 2026 12:19
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

No reviews

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

@fevac @kristinebilgrav