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vib-singlecell-nf
/
vsn-pipelines
A repository of pipelines for single-cell data in Nextflow DSL2
GNU General Public License v3.0
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Develop for v0.27.0
#358
Closed
dweemx
closed
2 years ago
dweemx
commented
3 years ago
Summary of changes
Move to new config structure Closes #310 #314 e8b377d [BREAKING CHANGE]
Add version check #355
Fix bug
sra
pipeline not working for scATAC-seq data Closes #348
Add multi-sample QC workflow 7f7c630
[sratoolkit] Add
maxSize
option (
-X
option of
prefetch
) b5c7bae. This option should be set accordingly when running
sra
pipeline.
Update Scanpy version to 1.8.1 #324 8370443
[scanpy] Allow to set perplexity parameter for t-SNE e3b256a
[scanpy] Implement additional flavors for computing HVG. Now possible to use:
seurat
,
seurat_v3
and
cell_ranger
[scrublet] Update Scrublet Dockerfile to 0.2.3 8370443
[harmony] Update Harmony to 1.0-3 74371bf
[pcacv] Save PRESS errors in case it fails finding the optimal number of PCs 742f3bd
Summary of changes
srapipeline not working for scATAC-seq data Closes #348maxSizeoption (-Xoption ofprefetch) b5c7bae. This option should be set accordingly when runningsrapipeline.seurat,seurat_v3andcell_ranger