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Enhancement/cancer type parameter reporting in ORANGE #126

Merged
merged 1 commit into from
Feb 17, 2025
Merged

Enhancement/cancer type parameter reporting in ORANGE #126

merged 1 commit into from
Feb 17, 2025

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rhassaine
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nf-core/oncoanalyser pull request

PR checklist

  • This comment contains a description of changes (with reason).
    Utils.groovy
  • New getCancerType method to provide user-provided doid data in the metamap for the ORANGE process to use
  • Added CancerType check during development

Modules > Local > Orange>main.nf

  • Included cancer_type as a value input in ORANGE process
  • Provided doid_arg in ORANGE command

Subworkflows > orange_reporting > main.nf

  • Added the cancer_type information in the orange process metamap (as well as overarching metamap)

nf-core pipelines linting

  • nextflow.config > Adjusted profile loading syntax (caused failed tests)
  • .nf-core.yml > nextflow config (params compute resources maximums) scope was causing issues (params.max_cpus, params.max_memory, params.max_time), skipped specifically
    & files_unchanged + actions_awsfulltest set to false
    & files_exist, included lib folder (only Utils, WorkflowMain, WorkflowOncoanalyser

*Additionally: ran the nf-core pipelines lint --dir . --fix files_unchanged and caused some cascading changes to meet nf-core standards and pass linting tests

  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>)

@rhassaine rhassaine added the enhancement New feature or request label Jan 27, 2025
@rhassaine rhassaine requested a review from scwatts January 27, 2025 14:08
@rhassaine rhassaine self-assigned this Jan 27, 2025
@github-actions GitHub Actions
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github-actions bot commented Jan 27, 2025 •
edited by nf-core-bot
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@github-actions GitHub Actions
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github-actions bot commented Jan 27, 2025 •
edited
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 61d1554

+| ✅ 201 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  18 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • 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 main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • schema_params - Schema param panel not found from nextflow config
  • schema_params - Schema param fastp_umi_location not found from nextflow config
  • schema_params - Schema param fastp_umi_length not found from nextflow config
  • schema_params - Schema param fastp_umi_skip not found from nextflow config
  • schema_params - Schema param markdups_umi_duplex_delim not found from nextflow config
  • schema_params - Schema param genome_version not found from nextflow config
  • schema_params - Schema param genome_type not found from nextflow config
  • schema_params - Schema param ref_data_hmf_data_path not found from nextflow config
  • schema_params - Schema param ref_data_panel_data_path not found from nextflow config
  • schema_params - Schema param ref_data_virusbreakenddb_path not found from nextflow config
  • schema_params - Schema param ref_data_genome_gtf not found from nextflow config
  • schema_params - Schema param ref_data_hla_slice_bed not found from nextflow config

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2025-01-31 12:19:03

@rhassaine rhassaine changed the base branch from master to dev January 27, 2025 14:09
scwatts
scwatts requested changes Jan 28, 2025
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@scwatts scwatts left a comment

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Thanks for the PR Rayan, can you please:

  • remove any user specific code (e.g. new .gitignore entries)
  • remove any unused, commented code
  • squash codes changes into a single commit (changes for linting shouldn't be needed)
  • and apply to the dev branch then force push to your branch

The above should simplify resolving merge conflicts and git history. I've also left some misc comments throughout. Once that is done can you check whether this runs as expected and provide a set of example commands to replicate?

@rhassaine rhassaine linked an issue Jan 29, 2025 that may be closed by this pull request
Add cancer_type parameter #121
Open
@rhassaine rhassaine force-pushed the enhancement/cancer-type-parameter-reporting branch from 8457d6b to 6255968 Compare January 31, 2025 00:01
@rhassaine rhassaine force-pushed the enhancement/cancer-type-parameter-reporting branch from 6255968 to 61d1554 Compare January 31, 2025 12:17
@scwatts
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scwatts commented Feb 17, 2025

The 'nf-core CI Run pipeline' check is failing due to an issue related to Nextflow version and nf-core template version that has been resolved in dev, forcefully merging into dev

@scwatts scwatts merged commit 93ebe95 into nf-core:dev Feb 17, 2025
4 of 6 checks passed
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@scwatts scwatts scwatts approved these changes

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Add cancer_type parameter
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@rhassaine @scwatts