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vib-singlecell-nf
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vsn-pipelines
A repository of pipelines for single-cell data in Nextflow DSL2
GNU General Public License v3.0
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Atacflow
#398
ghuls
opened
1 year ago
0
Bump ipython from 7.20.0 to 8.10.0 in /src/scanpy
#397
dependabot[bot]
opened
1 year ago
0
Bump certifi from 2020.12.5 to 2022.12.7 in /src/scanpy
#396
dependabot[bot]
opened
1 year ago
0
Bump pillow from 8.1.0 to 9.3.0 in /src/scanpy
#395
dependabot[bot]
opened
1 year ago
0
Bump joblib from 1.0.1 to 1.2.0 in /src/scanpy
#394
dependabot[bot]
opened
2 years ago
0
Convert NaNs from annotation
#393
s-aibar
opened
2 years ago
1
throw new Exception("Cannot append SCENIC loom to SCope loom because the IDs do not match.")[BUG]
#392
LinearParadox
opened
2 years ago
6
Bump nbconvert from 6.0.7 to 6.5.1 in /src/scanpy
#391
dependabot[bot]
opened
2 years ago
0
Bump nbconvert from 6.0.7 to 6.3.0 in /src/scanpy
#390
dependabot[bot]
closed
2 years ago
1
Bump mistune from 0.8.4 to 2.0.3 in /src/scanpy
#389
dependabot[bot]
opened
2 years ago
0
ARBORETO_WITH_MULTIPROCESSING fails to start
#388
GreyRockIQ
closed
2 years ago
0
pipeline executing error
#387
GreyRockIQ
closed
2 years ago
0
Bump lxml from 4.6.3 to 4.9.1 in /src/scanpy
#386
dependabot[bot]
opened
2 years ago
0
single-sample_test error
#385
GreyRockIQ
closed
2 years ago
0
Bump numpy from 1.21.0 to 1.22.0 in /src/scanpy
#384
dependabot[bot]
opened
2 years ago
0
Bcl2fastq implementation
#383
KrisDavie
closed
2 years ago
0
[BUG] Cannot invoke method containsKey() on null object
#382
AlinaKurjan
opened
2 years ago
2
[BUG] Unknown configuration profile: 'single_sample_decontx_scrublet'
#381
s-aibar
opened
2 years ago
0
Update scripts in singlecelltoolkit image to latest git version.
#380
ghuls
opened
2 years ago
0
Hotfix to lock nextflow version
#379
KrisDavie
closed
2 years ago
0
[BUG] Cannot invoke method containsKey() on null object
#378
HocheolJang426
opened
2 years ago
2
docker error unknown shorthand flag: 'B' in -B while running the pipeline
#377
MarcDalod
closed
2 years ago
1
[BUG] There is no package called "SeuratObject"
#376
alefrol638
opened
2 years ago
0
[BUG] scenic multirun stalls during Arboreto with multiprocessing
#375
Jay-Leung
opened
2 years ago
0
Bump pillow from 8.1.0 to 9.0.1 in /src/scanpy
#374
dependabot[bot]
closed
1 year ago
1
FATAL: container creation failed: mount
#373
gianfilippo
opened
2 years ago
2
Include statement is not allowed within a workflow definition
#372
gianfilippo
closed
2 years ago
2
Bump ipython from 7.20.0 to 7.31.1 in /src/scanpy
#371
dependabot[bot]
closed
1 year ago
1
Bump pillow from 8.1.0 to 9.0.0 in /src/scanpy
#370
dependabot[bot]
closed
2 years ago
1
[BUG] Include statement is not allowed within a workflow definition
#369
matt-sd-watson
opened
2 years ago
9
Bump lxml from 4.6.3 to 4.6.5 in /src/scanpy
#368
dependabot[bot]
closed
2 years ago
1
[SUGGESTION] Add Median genes/UMIs to Reporting
#367
KrisDavie
opened
2 years ago
0
Bump pillow from 8.1.0 to 8.3.2 in /src/scanpy
#366
dependabot[bot]
closed
2 years ago
1
SC__SCANPY__DIM_REDUCTION: nComps is both statically and dynamically[BUG]
#365
Zifeng-L
closed
2 years ago
2
Failed to find loop device[BUG]
#364
Zifeng-L
opened
2 years ago
0
[BUG] Error: Cannot append SCENIC loom to SCope loom because the IDs do not match
#363
iUser1234
opened
2 years ago
0
Develop_atac
#362
KrisDavie
closed
2 years ago
0
Fix harmony_only workflow
#361
KrisDavie
closed
3 years ago
0
[BUG] Failing to parse SRA metadata
#360
dweemx
opened
3 years ago
0
[BUG] loomHandler.nf - process PUBLISH_LOOM record container is missing
#359
Hynst
opened
3 years ago
0
Develop for v0.27.0
#358
dweemx
closed
2 years ago
0
Fixes a bug not able to use seurat_v3 flavor Scanpy in hvg selection
#357
dweemx
closed
3 years ago
0
Test nextflow update
#356
KrisDavie
closed
3 years ago
0
Implement check for config version
#355
KrisDavie
closed
3 years ago
0
Using flavor='seurat_v3' for feature selection may give better results [SUGGESTION]
#354
cbravo93
opened
3 years ago
2
Scrublet: ValueError: columns overlap but no suffix specified: Index(['nGene', 'nUMI'], dtype='object') [BUG]
#353
cbravo93
opened
3 years ago
1
[SUGGESTION] Handle both verisons of HyDrop ATAC
#352
cflerin
closed
2 years ago
0
[SUGGESTION] Take 10x Multiome data as inputs
#351
cflerin
opened
3 years ago
0
[SUGGESTION] Input of MEX files from non-cellranger formats
#350
cflerin
opened
3 years ago
0
Feat/348 sra nxf workflow for scatac
#349
dweemx
closed
3 years ago
0
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