Dev - GEX QC and Aggregate, BAM, and Clean-Up #2

chenv3 · 2023-11-17T19:21:28Z

GEX Initial QC with Seurat
GEX Initial QC Sample Report
Turn off automatic BAM creation
- Add create-bam flag to create BAM file
- Applies to:
  - GEX
  - CITE
  - MULTI
Add GEX aggregate flag
- Choose between mapped and none for read depth normalization
Automatic clean-up of intermediate Cell Ranger folder for all pipelines
Edit summary report script to not check for intermediate folder and to keep 10x column header order for additional columns

…ing a sample name sort for generateSummaryFiles.py

…l sample QC

…at QC report is run to prevent parallel jobs from interfering with each other

…or aggrgate and create-bam flags to GEX pipeline so that Cell Ranger aggregate only runs when flag is used and no bam file is created by default

…ine BAM file generation to off by default and add support for create-bam flag

… ranger folder, and base and ATAC versions had column header code edited to keep 10x column header order for additional columns

…fault and add support for create-bam flag

…ring

chenv3 added 18 commits October 11, 2023 17:14

Minor updates to summary file scripts changing python version and add…

66c6872

…ing a sample name sort for generateSummaryFiles.py

Add script to create CSV file to run GEX aggregate

964166c

Add filter flag to pipeline and handle it in Snakefile

ea9dedb

Add aggregate and initial QC to GEX pipeline; add R script for initia…

0e82724

…l sample QC

Add report for initial GEX sample QC

e5dda37

Add cell filter summary for GEX samples

383fbcd

Add cluster configuration for GEX seuratQC rule

c61ddab

Extract tmpdir config parameter in Snakefile; Change how the GEX Seur…

4d434d0

…at QC report is run to prevent parallel jobs from interfering with each other

Add aggregate and create-bam flags to pipeline wrapper; add support f…

0993ee0

…or aggrgate and create-bam flags to GEX pipeline so that Cell Ranger aggregate only runs when flag is used and no bam file is created by default

Add cleanup rules for GEX pipeline

debd415

Add eample of filter flag in help documentation

3da4d7c

Add sample cleanup rules to CITE and VDJ pipelines; Change CITE pipel…

241dad4

…ine BAM file generation to off by default and add support for create-bam flag

Edit generate summary file scripts to not check for intermediate cell…

4e8e51a

… ranger folder, and base and ATAC versions had column header code edited to keep 10x column header order for additional columns

Add cleanup functionality to ATAC pipeline

62441bb

Add cleanup functionality and change BAM file generation to off by de…

8265e30

…fault and add support for create-bam flag

Add intermediate folder cleanup to multiome pipeline

e387da2

seuratSampleQC.R - fix typo and add additional resolutions for cluste…

bb46f15

…ring

Update run documentation and organizing flags by version

b8ed5df

chenv3 changed the title ~~GEX QC and Aggregate, BAM, and Clean-Up~~ Dev - GEX QC and Aggregate, BAM, and Clean-Up Nov 17, 2023

chenv3 merged commit 75e355d into main Nov 20, 2023
2 checks passed

chenv3 deleted the dev branch December 18, 2023 16:46

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Dev - GEX QC and Aggregate, BAM, and Clean-Up #2

Dev - GEX QC and Aggregate, BAM, and Clean-Up #2

chenv3 commented Nov 17, 2023

Dev - GEX QC and Aggregate, BAM, and Clean-Up #2

Dev - GEX QC and Aggregate, BAM, and Clean-Up #2

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chenv3 commented Nov 17, 2023