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

Add rnaseq input #174

Open
wants to merge 8 commits into
base: dev
Choose a base branch
from
Open

Add rnaseq input #174

wants to merge 8 commits into from

Conversation

christopher-mohr
Copy link
Collaborator

@christopher-mohr christopher-mohr commented Aug 25, 2022 •
edited
Loading

This adds the option to provide expression values for the peptide prediction and includes the following changes

  • adapt sample sheet check
  • handle expression file along channels and add it to epytope_peptide_prediction
  • add functionality in epaa.py for parsing the expression values and mapping it to the peptide predictions.

Currently the expected format of the provided expression values is the one generated by salmon as given in the rnaseq pipeline on merged transcript/gene level.

We still need functionality from epytope that will come with the next release.

Resolves #134.

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>).
  • 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).

@christopher-mohr christopher-mohr added this to the 2.2.0 milestone Aug 25, 2022
@github-actions
Copy link

github-actions bot commented Aug 25, 2022 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e308d92

+| ✅ 160 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowEpitopeprediction.groovy: Optionally add in-text citation tools to this list.

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-14 07:02:04

jonasscheid
jonasscheid reviewed Aug 25, 2022
View reviewed changes
Copy link
Contributor

@jonasscheid jonasscheid left a comment

Choose a reason for hiding this comment

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

Some suggestions regarding the optional handling of the expression column in the sample sheet

bin/epaa.py Show resolved Hide resolved
bin/check_samplesheet.py Outdated Show resolved Hide resolved
modules/local/epytope_peptide_prediction.nf Show resolved Hide resolved
@christopher-mohr
Copy link
Collaborator Author

Unfortunately, another Ensembl archive has been removed for GRCh38, which is the reason why the grch38 test failed. I updated the used archive to the next available one for now. We will improve the interface to Ensembl biomart with the next epytope release for which I already rewrote the biomart adapter.

jonasscheid
jonasscheid approved these changes Aug 25, 2022
View reviewed changes
Copy link
Contributor

@jonasscheid jonasscheid left a comment •
edited
Loading

Choose a reason for hiding this comment

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

Comments discussed and resolved ✅ LGTM

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jonasscheid jonasscheid jonasscheid approved these changes

Assignees
No one assigned
Labels
do not merge
Projects
None yet
Milestone
2.2.0
Development

Successfully merging this pull request may close these issues.
2 participants
@christopher-mohr @jonasscheid