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

Handle fasta #266

Merged
merged 8 commits into from
Jan 31, 2025
Merged

Handle fasta #266

merged 8 commits into from
Jan 31, 2025

Conversation

jonasscheid
Copy link
Contributor

@jonasscheid jonasscheid commented Jan 31, 2025 •
edited
Loading

Another overhaul PR:

  • Updated and optimized EPYTOPE_GENERATE_PEPTPIDES and replaced with FASTA2PEPTIDES module. This module generates now peptide tsv files and writes one file per length depeding on min_peptide_length_classI/II-min_peptide_length_classI/II. Tested this script with Full swissport and seems to work quite nicely regarding runtime and RAM usage and file sizes are almost equal with this.
  • Optimize SPLIT_PEPTIDES module such that it takes any input file directly before MHC_BINDING_PREDICTION subworfklow
  • Introduced meta.file_id to track and properly merge multi prediciton files per splitted file in MHC_BINDING_PREDICTION
  • Introduced optional wide_format_output to transform output format to predictor_allele_bindingMetric rather then default long format
  • Cleaned up outdated code

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/epitopeprediction branch on the nf-core/test-datasets repository.
  • 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).

@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 Jan 31, 2025 •
edited
Loading

nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 677fc65

+| ✅ 208 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   1 tests had warnings |!
-| ❌   2 tests failed       |-

❌ Test failures:

  • nextflow_config - Config default value incorrect: params.tools is set as syfpeithi in nextflow_schema.json but is mhcflurry in nextflow.config.
  • nextflow_config - Config default value incorrect: params.peptides_split_minchunksize is set as 5000 in nextflow_schema.json but is 500 in nextflow.config.

❗ Test warnings:

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-epitopeprediction_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-epitopeprediction_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-epitopeprediction_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2025-01-31 12:59:39

@jonasscheid jonasscheid merged commit 048e86d into nf-core:mhc-binding-subworkflow Jan 31, 2025
2 of 18 checks passed
@jonasscheid jonasscheid deleted the handle-fasta branch January 31, 2025 14:27
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
@jonasscheid @nf-core-bot