add pseudobulk tests#83
Open
dimalvovs wants to merge 4 commits into
Open
Conversation
Unit Test Results11 tests 11 ✅ 2m 48s ⏱️ Results for commit 6f399eb. ♻️ This comment has been updated with latest results. |
Contributor
There was a problem hiding this comment.
Pull request overview
This PR expands the test suite to cover a pseudobulk-style single-cell dataset by adding a new multi-sample/multi-patient samplesheet and new nf-test cases, alongside additional single-cell phenotype test data.
Changes:
- Added a new pseudobulk samplesheet for patients P001/P002 under
tests/test_data/sc_test_data/. - Added nf-test coverage for running the main pipeline with the new pseudobulk samplesheet.
- Added a samplesheet-checking nf-test for the pseudobulk samplesheet, and introduced an additional scRNAseq phenotype CSV test dataset.
Reviewed changes
Copilot reviewed 3 out of 15 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
tests/test_data/sc_test_data/scRNAseq_TCR_phenotypes.csv |
Adds scRNAseq barcode→cell-type mapping data (currently not referenced by tests/code). |
tests/test_data/sc_test_data/samplesheet_P001_P002.csv |
Adds a multi-patient pseudobulk samplesheet pointing to local AIRR TSV test inputs. |
tests/modules/local/samplesheet/samplesheet_check.nf.test |
Adds a new nf-test case for validating pseudobulk samplesheet processing (currently references a non-existent path). |
tests/main.nf.test |
Adds a pipeline-level nf-test that runs the workflow using the new pseudobulk samplesheet. |
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
Comment on lines
+149
to
+152
| process { | ||
| """ | ||
| input[0] = file("${projectDir}/tests/test_data/sc_test_data/samplesheets/samplesheet_P001_P002.csv") | ||
| """ |
Comment on lines
+1
to
+3
| barcode,sctype | ||
| GBM1-DFCI1-S1-TCR-LIB_AAACGGGGTAATAGCA-1,Stress_sig | ||
| GBM1-DFCI1-S1-TCR-LIB_AAAGCAACAAGACGTG-1,CD8_cytotoxic |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
This pull request adds new test coverage for pseudobulk single-cell datasets by introducing a dedicated samplesheet and corresponding tests for both the overall pipeline and the samplesheet checking process. These changes help ensure that the workflow and its components correctly handle pseudobulk input data.
New test data and coverage for pseudobulk datasets:
samplesheet_P001_P002.csvcontaining multiple patient and sample records for testing single-cell pseudobulk scenarios.Pipeline and process test enhancements:
main.nf.testthat runs the pipeline using the new pseudobulk samplesheet and checks for successful completion.samplesheet_check.nf.testto verify that the samplesheet checking process correctly processes the new pseudobulk samplesheet and produces the expected output.