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Version 3 Update#6

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chenv3 merged 16 commits intomainOpenOmics/cell-seek:mainfrom devOpenOmics/cell-seek:devCopy head branch name to clipboardJan 9, 2025

+1,822-149

Commits

Commits on Aug 5, 2024

• Add forcecells flag to ATAC, CITE, GEX, and MULTI pipelines

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Commits on Sep 3, 2024

• First pass for adding Cellranger output as potential pipeline input

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Commits on Sep 17, 2024

• Set max mitochondrial upper to 100%

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• Add script for analysis of samples from cite pipeline and resulting QC report

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Commits on Nov 20, 2024

• Add QC reports to cite pipeline; edited cite QC to make hashtag plot conditional and fix command to get list of resolutions

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Commits on Dec 17, 2024

• Add script for cite pipeline summary report, change R version to being stored in module.json and update from 4.3.0 to 4.4.0, add in option for cellranger 9.0.0

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• Add summary integration report

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Commits on Dec 26, 2024

• Fix errors in integration rules and report

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Commits on Dec 27, 2024

• Add Cell Ranger 9.0.0 to documentation, and integrate report copy rule to gex pipeline

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Commits on Jan 6, 2025

• Fix typo in documentation

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Commits on Jan 8, 2025

• Edit cite QC script to fix errors in HTO code

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• Change seuratIntegrate to run on largemem

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• Add ability to start pipeline from cell ranger output, edit documentation for this new input, change pipeline rules to keep condition cell ranger input on the same line as previous input

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Commits on Jan 9, 2025

• Bump version

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• Update test to check cellranger output functionality

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• Update main.yaml

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