Published December 3, 2021
| Version v0.27.0
Software
Open
vib-singlecell-nf/vsn-pipelines: v0.27.0
Description
Summary of changes
- Move to new config structure Closes #310 #314 e8b377d [BREAKING CHANGE]
- Include preliminary ATAC-seq workflows https://github.com/vib-singlecell-nf/vsn-pipelines/pull/362
- 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 ofprefetch
) b5c7bae. This option should be set accordingly when runningsra
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
andcell_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
Files
vib-singlecell-nf/vsn-pipelines-v0.27.0.zip
Files
(1.1 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/vib-singlecell-nf/vsn-pipelines/tree/v0.27.0 (URL)