Skip to content

Implement PEACH subworkflow #187

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
Open
wants to merge 5 commits into
base: dev
Choose a base branch
from
Open

Implement PEACH subworkflow #187

wants to merge 5 commits into from

Conversation

scwatts
Copy link
Collaborator

@scwatts scwatts commented Apr 11, 2025

No description provided.

@nf-core-bot
Copy link
Member

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
Copy link

github-actions bot commented Apr 17, 2025 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 66854cb

+| ✅ 197 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗  17 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • nextflow_config - Config manifest.version should end in dev: 2.0.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 redux_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_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 2025-04-22 05:05:12

@scwatts scwatts linked an issue Apr 23, 2025 that may be closed by this pull request
Implement PEACH #143
Open
@scwatts
Copy link
Collaborator Author

scwatts commented May 7, 2025

Force pushing with clean history rebased on top of dev

@scwatts scwatts force-pushed the peach-subworkflow branch from 66854cb to d10d9aa Compare May 7, 2025 04:51
@scwatts scwatts marked this pull request as ready for review May 7, 2025 05:13
@scwatts scwatts requested a review from qclayssen May 7, 2025 05:16
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@qclayssen qclayssen qclayssen 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.

Implement PEACH
3 participants
@scwatts @nf-core-bot @qclayssen