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Standardize h5ad/seurat var gene annotations across aligners
enhancement
New feature or request
#363
opened Aug 15, 2024 by
alexblaessle
nextflow inspect does not work due to missing parameters
bug
Something isn't working
#347
opened Jul 26, 2024 by
stevekm
cellranger count => Your reference does not contain the expected files
bug
Something isn't working
#345
opened Jul 11, 2024 by
nick-youngblut
Implement sample demultiplexing followed by VDJ + feature barcode analysis per sample
enhancement
New feature or request
#343
opened Jun 28, 2024 by
herpov
cellranger_count.py: capture stderr and stdout
enhancement
New feature or request
quality & consistency
improve quality and reduce maintenance burden
#341
opened Jun 24, 2024 by
nick-youngblut
Trimming R1 fast files in all aligners
enhancement
New feature or request
#333
opened May 24, 2024 by
ChristopherMancuso
cellranger-multi implementation follow-up
enhancement
New feature or request
#332
opened May 23, 2024 by
fmalmeida
5 tasks
Running 'cellranger-arc count' with existing genome index
enhancement
New feature or request
#331
opened May 17, 2024 by
ashwinikumarkulkarni
Sample merging does not work if files are named the same
bug
Something isn't working
bug-confirmed
#324
opened May 4, 2024 by
nick-youngblut
cellranger mkref with multiple species
enhancement
New feature or request
#319
opened Apr 16, 2024 by
MaestSi
cellranger_count.py: remove any existing output directory
enhancement
New feature or request
#315
opened Apr 9, 2024 by
nick-youngblut
Update to the latest simpleaf
enhancement
New feature or request
#312
opened Mar 5, 2024 by
DongzeHE
Clean up mtx conversion code
enhancement
New feature or request
quality & consistency
improve quality and reduce maintenance burden
#310
opened Mar 5, 2024 by
grst
When aligner is cellrangerarc the step MTX_TO_SEURAT failed
bug
Something isn't working
#299
opened Jan 31, 2024 by
wzheng0520
Utilize central modules for simpleaf workflow
enhancement
New feature or request
quality & consistency
improve quality and reduce maintenance burden
#296
opened Jan 23, 2024 by
apeltzer
Tests for cellranger-arc
enhancement
New feature or request
quality & consistency
improve quality and reduce maintenance burden
#290
opened Jan 18, 2024 by
grst
Update or remove universc
enhancement
New feature or request
quality & consistency
improve quality and reduce maintenance burden
#289
opened Jan 18, 2024 by
grst
Multi-omics support (meta-issue)
enhancement
New feature or request
#272
opened Oct 26, 2023 by
grst
1 of 3 tasks
Switch to use central nf-core modules
enhancement
New feature or request
quality & consistency
improve quality and reduce maintenance burden
#264
opened Sep 6, 2023 by
pinin4fjords
Error at SIMPLEAF_INDEX for user supplied genome/annotation
bug
Something isn't working
#253
opened Jul 19, 2023 by
jeremymsimon
Option to skip postprocessing
enhancement
New feature or request
#235
opened Jun 8, 2023 by
zvittorio
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