Issues: nf-core/scrnaseq
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'star' in genome configrations ignored
bug
Something isn't working
#327
opened May 9, 2024 by
pinin4fjords
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
allow use of .gz when specifying fast and gtf
enhancement
New feature or request
#313
opened Mar 20, 2024 by
ChristopherMancuso
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
Crash when specifying existing --star_index using star aligner
bug
Something isn't working
#277
opened Dec 15, 2023 by
ffmmulder
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
Support for 10x FFPE scRNA
enhancement
New feature or request
#247
opened Jul 3, 2023 by
pakiessling
Option to skip postprocessing
enhancement
New feature or request
#235
opened Jun 8, 2023 by
zvittorio
Universc "essential container in task exited"
bug
Something isn't working
#230
opened Jun 2, 2023 by
adamrtalbot
Support additional sequencing platforms through seqspec
enhancement
New feature or request
#212
opened Mar 23, 2023 by
grst
STARsolo Workflow Doesn't Output Solo.out counts
bug
Something isn't working
#187
opened Dec 8, 2022 by
sean-at-tessera
Include --expect-cells when using --aligner cellranger
enhancement
New feature or request
#182
opened Nov 11, 2022 by
adairama
Add Mermaid Graph to Readme for users
documentation
enhancement
New feature or request
#180
opened Nov 9, 2022 by
apeltzer
Reduce the number of published files from alevin-fry output
enhancement
New feature or request
good first issue
Good for newcomers
#178
opened Nov 6, 2022 by
tomsing1
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