UCSF-DSCOLAB data_processing_pipelines issues

UCSF-DSCOLAB / data_processing_pipelines

A repository to store the existing pipelines to process the various CoLabs datasets

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issues

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Additional logging

#85 erflynn opened 4 days ago
0
Stripping date-time to match md5s

#84 erflynn opened 4 days ago
0
MD5s for automated processing re-run do not match

#83 erflynn opened 1 week ago
10
Separate output for post-demuxlet

#82 erflynn opened 1 week ago
0
fixed bug in calculation for doublet stat .csv

#81 erflynn closed 1 week ago
3
single-cell additional info parsing

#80 dtm2451 opened 3 weeks ago
0
single-cell umap file name ambiguity

#79 dtm2451 opened 3 weeks ago
0
Isolated and more robust way to activate and use conda environments

#78 amadeovezz closed 1 month ago
0
Clean up of workflow, add tests for new functions

#77 erflynn opened 2 months ago
0
Testing snapshot stdout

#76 erflynn opened 2 months ago
0
sc-seq diagnostic plot improvements

#75 erflynn opened 2 months ago
0
Do not use a shared conda environment for running snakemake

#74 amadeovezz closed 1 month ago
0
Depooling pipeline does not leverage slurm

#73 amadeovezz opened 3 months ago
1
sc_seq pipeline diagnostic plots for nCount_ADT are unusable

#72 dtm2451 opened 3 months ago
0
cap nCount_ADT axis to 25000 in diagnostic plots

#71 dtm2451 opened 3 months ago
2
Incorporate major changes from single cell dev branch into main

#70 erflynn closed 2 months ago
1
Pull in more info per tcr and bcr clonotype

#69 dtm2451 opened 4 months ago
4
sc_seq pipeline should pull in or organize more TCR/BCR info

#68 dtm2451 opened 4 months ago
0
Bulk rnaseq multiqc per sample

#67 AlaaALatif opened 4 months ago
1
sc_seq pipeline fails due to missing process/function keySet()

#66 syellamilli closed 2 months ago
3
Test hotfix

#65 amadeovezz closed 7 months ago
1
Tests are not localized

#64 amadeovezz opened 7 months ago
0
Localized and self-contained tests

#63 amadeovezz closed 7 months ago
0
WIP: Add VDJ processing capabilities

#62 erflynn closed 5 months ago
0
pull in amazing cluster dispersion QC plots

#61 erflynn opened 7 months ago
1
Misc Run Setup: Add freecycle, adjust default errorStrategy, and fix resume/cleanup

#60 erflynn opened 7 months ago
7
Add info on toy VCF to example-inputs README

#59 erflynn closed 7 months ago
0
Simplify user configuration for reference genomes for bulk RNAseq

#58 AlaaALatif opened 8 months ago
0
Trace bug while running tests

#57 amadeovezz opened 8 months ago
0
Move paths to integration_test_user directory

#56 amadeovezz closed 8 months ago
1
Single-cell tests have harcoded paths

#55 amadeovezz opened 8 months ago
0
Forgot test config file

#54 amadeovezz closed 8 months ago
0
De-pooling pipeline

#53 amadeovezz closed 3 months ago
9
post-merge filtering of variants in bulk pipeline

#52 erflynn opened 8 months ago
1
Re-start after Dsc-pileup or merge

#51 erflynn opened 8 months ago
0
Get nextflow to submit to specified partition

#50 erflynn opened 8 months ago
1
Seperate out Freemuxlet and Demuxlet into two composable pipelines

#49 amadeovezz opened 8 months ago
0
Improve test cases for single cell

#48 amadeovezz opened 8 months ago
2
fix run_resume.sh script

#47 erflynn opened 8 months ago
0
Add test snapshots, and fix another demuxlet bug

#46 amadeovezz closed 8 months ago
0
Update pre-fmx-qc option to match pre-qc

#45 erflynn opened 8 months ago
0
working commit of the fmx-assign-to-gt functionality

#44 erflynn opened 8 months ago
3
Check if we can set a limit to resources consumed by nextflow

#43 amadeovezz opened 8 months ago
1
WIP: Demuxlet fixes

#42 amadeovezz closed 8 months ago
1
Deletes working during if OOT error

#41 erflynn opened 8 months ago
1
Pipeline steps do not run after DEMUXLET

#40 amadeovezz closed 8 months ago
0
Make outputs sync with metis model for bulk

#39 erflynn opened 8 months ago
1
dsc pileup output always written to freemuxlet

#38 erflynn closed 8 months ago
0
De-pool piepline for fully demultiplexed scRNAseq data

#37 dtm2451 opened 9 months ago
2
Single cell: Refactor post_qc to use new json config, and some slight refactoring

#36 amadeovezz closed 9 months ago
3