Published December 3, 2021 | Version v0.27.0
Software Open

vib-singlecell-nf/vsn-pipelines: v0.27.0


Summary of changes

  • Move to new config structure Closes #310 #314 e8b377d [BREAKING CHANGE]
  • Include preliminary ATAC-seq workflows
  • 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



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