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Version 3 Update #6
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Collaborator
chenv3
commented
Jan 9, 2025
- Added in a force cells flag which can be applied to the following pipelines
- GEX
- CITE
- MULTI
- ATAC
- Added support for additional version to cellranger flag for GEX, CITE, VDJ, and MULTi pielines
- Also handles version 9.0.0
- Added support for running pipeline on Cell Ranger output
- Changed cellranger calls so optional flags are on the same line as the last required flag
- Edits to GEX pipeline
- Changed to running Seurat v5 using R4.4.0
- Set an upper limit of 100 for mitochondrial filter threshold
- Added in Seurat integration for normalization and SCTransform. Runs if more than one sample is processed
- CCA
- Joint PCA
- RPCA
- Harmony
- Create a summary integration report
- Edits to CITE pipeline
- Add basic Seurat QC analysis
- If hashtags are run with the name starting with “HTO-” or “HTO_‘, will try to run hashtag demultiplexing
…conditional and fix command to get list of resolutions
…g stored in module.json and update from 4.3.0 to 4.4.0, add in option for cellranger 9.0.0
…e to gex pipeline
…tion for this new input, change pipeline rules to keep condition cell ranger input on the same line as previous input
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