Version 2 Update #5
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chenv3
commented
Apr 17, 2024
•
chenv3
commented
- Change version flag to pipeline flag
- Add cellranger flag to select version for GEX, CITE, VDJ, and MULTI pipelines
- Handles version 7.1.0, 7.2.0, and 8.0.0
- Add 2024 genome release for GEX, CITE, and MULTI pipelines
- Add custom json support for genome
- GEX add QC Summary report
- Edit MULTI summary report to include sheet for FASTQ QC output
- Edits to GEX QC analysis
- Add silhouette analysis for GEX QC cluster resolutions
- Add metadata parameter to add sample level metadata to Seurat object
- Fix error to add back in cut-off line to pre-filter QC plots
- Edit GEX QC report
- Add support for silhouette analysis
- Add explanation text for when adaptive thresholds are used
- Edit multiconfig to be compatible with Cell Ranger 8.0.0
- Add rename flag for GEX, VDJ, ATAC pipelines
- Only runs the samples that are included in the rename file
…J, MULTI) and the 10x newly released 2024 references. Changing version flag to pipeline to avoid confusion, and adding in cellranger flag for selecting cellranger version. Adding in checks features and hashtag file formats, and conditionally required flags.
Import run.md updates
…vel metadata when performing initial QC and output sessionInfo log file
… FASTQ related statistics reported in multi metric summary
…es, add UMAP filter plot
… list in seuratQCSummaryReport
Add the functionality to supply metadata file for GEX pipeline. Also add support for providing custom json file for the genome flag
Editing cell-seek pipeline to add a genome option to help create a custom reference json file
Documentation updated to include the new genome command. Bumping the version to 2.0.0 in preparation of release
…ed UMAP Seurat QC, report, and summary report edited to handle the new QC plot for both pre and post-filter plots. Silhouette scores added to seurat QC and seurat QC report. Cleaned up summary report of commented commands.
…tation gex.smk - edited to copy QC reports to final reports folder; add in a defaultFilter flag for QC report generation seuratSampleQC.R - add comment seuratSampleQCReport.Rmd - add defaultFilter flag to edit report text and reference depending on if adaptive threshold or filter file threshold was used; add additional documentation for silhouette score / plots seuratSampleQCSummaryReport.Rmd - clustering plot will try to plot resolution with highest silhouette score if silhouette scores are calculated run.md - minor updates to documentation providing links to genome command for custom reference json
skchronicles
approved these changes
Apr 18, 2024
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Nice, this will be super useful!
atac.smk, gex.smk, vdj.smk, Snakefile - Added the rename ability to VDJ and ATAC and make the pipelines consistent in parameter names genome.json - mm2024 vdj was previously accidentally pointing to human reference, mixed to point to mouse cell-seek and run.py - add in test to check the rename file format and check to see if input FASTQ files are included in the rename / libraries files; also throws an error if detects that rename / libraries is trying to call a FASTQ file not in the input run.md - documentation added to include the rename flag for GEX, VDJ, and ATAC
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