Sync changes from development with main for v0.8.0
#728
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…annotation columns to retain
… NA confusion, especially with singler which CAN assign NAs
…pes-during-merge Keep cell type columns when merging
…metadata-from-merged
…olumns-when-merging Retain filter columns when merging
…data-gene_ids Don't rename rowdata `gene_ids` column
…in-check Fix merge.nf workflow adt and multiplex check
…e-unlassified Actually remove unclassified cells from heatmap
…er a string, or named vector if there are multiple samples (multiplex)
Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
…w-figure Update overview figure
Add nextflow_schema.json file
Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
Handle empty sample type columns and add sentence about references not having tumor cells
Use `mem_max` for all merging and sync changes from `main`
Update version tag and scpcaTools container
updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.0 → v0.3.2](astral-sh/ruff-pre-commit@v0.3.0...v0.3.2) - [github.com/pre-commit/mirrors-prettier: v3.0.3 → v4.0.0-alpha.8](pre-commit/mirrors-prettier@v3.0.3...v4.0.0-alpha.8)
jashapiro
approved these changes
Mar 13, 2024
.pre-commit-config.yaml
Outdated
| @@ -30,7 +32,7 @@ repos: | |||
| args: [--update-only, --title=**Table of Contents**] | |||
| - repo: https://github.com/astral-sh/ruff-pre-commit | |||
| # Ruff for linting and formatting python | |||
| rev: v0.2.1 | |||
| rev: v0.3.0 | |||
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| rev: v0.3.0 | |
| rev: v0.3.2 |
[pre-commit.ci] pre-commit autoupdate
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In preparation for #654, this syncs all changes from
developmenttomain. This includes the merge workflow, updates to cell typing, and rds file compression.