feature branch: nice-to-have features#84
Draft
emmcauley wants to merge 2 commits into
Draft
Conversation
|
Collaborator
|
@coderabbitai review |
✅ Actions performedReview triggered.
|
📝 WalkthroughWalkthroughThis pull request introduces skip parameters for CNV, MSI, and TMB analysis steps, raising the TMB variant allele frequency threshold from 0.05 to 0.10, and refactoring the CIViCpy workflow. Key changes include pinning GitHub Actions dependencies, adding a new CIVICPY_UPDATE_CACHE process, renaming CIVICPY to CIVICPY_ANNOTATE_VCF, updating CIViCpy container to version 5.2.0, and adding conditional execution gates across multiple analysis processes. gnomAD frequency field mappings are updated, and configuration files are adjusted to support selective pipeline component execution. 🚥 Pre-merge checks | ✅ 1 | ❌ 2❌ Failed checks (2 inconclusive)
✅ Passed checks (1 passed)
✏️ Tip: You can configure your own custom pre-merge checks in the settings. ✨ Finishing Touches📝 Generate docstrings
🧪 Generate unit tests (beta)
Tip 💬 Introducing Slack Agent: The best way for teams to turn conversations into code.Slack Agent is built on CodeRabbit's deep understanding of your code, so your team can collaborate across the entire SDLC without losing context.
Built for teams:
One agent for your entire SDLC. Right inside Slack. Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out. Comment |
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Actionable comments posted: 1
🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.
Inline comments:
In `@conf/test.config`:
- Around line 45-48: The test profile disables the CIVICPY cache task via the
withName block for "CIVICPY_UPDATE_CACHE" (ext.when = { false }) but doesn't set
params.skip_civicpy, so the workflow still tries to run CIViCPY steps; update
the test profile params to add skip_civicpy = true (i.e., set
params.skip_civicpy) so the workflow's if (!params.skip_civicpy) gating will
skip the CIVICPY path consistently with the cache task being disabled.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
ℹ️ Review info
⚙️ Run configuration
Configuration used: Organization UI
Review profile: CHILL
Plan: Pro
Run ID: f01910e6-1211-4f69-9dab-eff5411610b6
📒 Files selected for processing (16)
.github/workflows/linting.yml.github/workflows/twistgp_ci.ymlCHANGELOG.mdREADME.mdassets/pytmb_vep.ymlconf/modules.configconf/test.configmodules/local/civicpy/annotate/environment.ymlmodules/local/civicpy/annotate/main.nfmodules/local/civicpy/annotate/meta.ymlmodules/local/civicpy/update_cache/main.nfmodules/local/civicpy/update_cache/meta.ymlmodules/local/tmb/main.nfnextflow.confignextflow_schema.jsonworkflows/twistcgp.nf
Comment on lines
+45
to
48
| withName: "CIVICPY_UPDATE_CACHE" { | ||
| // Downloading the CIViC cache is too slow for CI | ||
| ext.when = { false } | ||
| } |
There was a problem hiding this comment.
🧩 Analysis chain
🏁 Script executed:
#!/bin/bash
set -euo pipefail
echo "== test profile civicpy-related config =="
rg -n -C2 'CIVICPY_UPDATE_CACHE|skip_civicpy|skip_tmb|skip_msi|ext.when' conf/test.config
echo
echo "== workflow civicpy wiring =="
rg -n -C2 'if \(!params.skip_civicpy\)|CIVICPY_UPDATE_CACHE|CIVICPY_ANNOTATE_VCF' workflows/twistcgp.nfRepository: fulcrumgenomics/twistcgp
Length of output: 2625
Fix CIVICPY test-profile gating mismatch.
Disabling CIVICPY_UPDATE_CACHE with ext.when = { false } (line 45) leaves the workflow trying to use a nonexistent cache output since skip_civicpy is not set in params. The workflow's if (!params.skip_civicpy) check will still attempt to run CIVICPY processes; set skip_civicpy = true in the test profile params (line 52) to properly gate the entire CIVICPY path.
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.
In `@conf/test.config` around lines 45 - 48, The test profile disables the CIVICPY
cache task via the withName block for "CIVICPY_UPDATE_CACHE" (ext.when = { false
}) but doesn't set params.skip_civicpy, so the workflow still tries to run
CIViCPY steps; update the test profile params to add skip_civicpy = true (i.e.,
set params.skip_civicpy) so the workflow's if (!params.skip_civicpy) gating will
skip the CIVICPY path consistently with the cache task being disabled.
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
2 participants
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.
Constituent PRs