Releases: AlexsLemonade/scpca-nf
Releases · AlexsLemonade/scpca-nf
scpca-nf v0.8.4
What's Changed
Bug fix release:
- Only count single cell libraries for max merged
- Account for different HVG name in merged object
Full Changelog: v0.8.3...v0.8.4
scpca-nf v0.8.3
What's Changed
-
Updates to
AnnData
objects:- PCA and UMAP embeddings are now stored as
X_pca
andX_umap
(previouslyX_PCA
andX_UMAP
) .var
contains ahighly_variable
column indicating which genes are part of the list of highly variable genes.uns
contains apca
object with parameters and variance weights associated with the PCA embeddings
- PCA and UMAP embeddings are now stored as
-
Addition of a
max_merge_libraries
parameter formerge.nf
to limit the number of libraries that can be merged into a single object.
Full Changelog: v0.8.2...v0.8.3
scpca-nf v0.8.2
What's Changed
- Use new, slimmer
scpcaTools
docker containers (see https://github.com/AlexsLemonade/scpcaTools/releases/tag/v0.4.0) - Bulk files,
bulk_quant.tsv
andbulk_metadata.tsv
, are now saved to abulk
directory - Main QC reports and cell type reports now include a table summarizing sample metadata (age, sex, diagnosis, etc.)
Full Changelog: v0.8.1...v0.8.2
scpca-nf v0.8.1
What's Changed
- Output HDF5 files now have the
.h5ad
extension instead of.hdf5
- Bug fixes:
- Skip running
CellAssign
if a processed object only has 1 cell - No cell type reports are created if processed objects only have 1 cell
- Make sure to account for no genetic demultiplexing when estimating sample cell counts for
metadata.json
- Skip any downstream processing if no cells are left after filtering out empty droplets
- Skip running
Full Changelog: v0.8.0...v0.8.1
scpca-nf v0.8.0
What's Changed
- Addition of
merge.nf
used to create mergedSingleCellExperiment
andAnnData
objects- The merged workflow takes as input a list of projects and creates a single merged object for each project
- Also includes a report, summarizing the contents of the merged object
- Some minor aesthetic fixes to cell type report
- Use
bz2
compression to reduce file sizes forSingleCellExperiment
objects - Add
nextflow_schema.json
to repo
Full Changelog: v0.7.3...v0.8.0
scpca-nf v0.7.3
What's Changed
- Skip any additional processing (clustering, cell type assignment) for processed objects with 0 cells
- Use new
max_mem
label forCellAssign
classification, which usesparams.max_memory
after the first failure.
Full Changelog: v0.7.2...v0.7.3
scpca-nf v0.7.2
What's Changed
- Skip
CellAssign
if too few cells - Small bug fixes for running multiplexed samples through cell typing
- Skip cell typing for cell line samples
- Small adjustments to UMAPs in the cell typing report
- Account for missing input files
Full Changelog: v0.7.1...v0.7.2
scpca-nf v0.7.1
What's Changed
- Update memory and CPU requests for running
CellAssign
- Set max retries after AWS instance failure to 2
- Use On Demand instances on 3rd retry
- Create faceted UMAPs in cell type report
Full Changelog: v0.7.0...v0.7.1
scpca-nf v0.7.0
What's Changed
- Addition of cell type annotation to the main workflow, including:
- Annotation with either
SingleR
orCellAssign
- New output that includes a processed
SingleCellExperiment
andAnnData
objects with cell type annotations and a cell type summary report - Documentation for adding cell type annotations
- Annotation with either
- By default, cell type annotation is turned off. To run the workflow with cell type annotation, use the
--perform_celltyping
flag. - By default, if cell typing results already exist, previous results are used. The
--repeat_celltyping
flag can be used to repeat previous cell type annotation. - Addition of pre-commit to the repo
Full Changelog: v0.6.3...v0.7.0
scpca-nf v0.6.3
What's Changed
- Make sure all RDS files are compressed
- Accommodate running multiple projects at once using the
--project
parameter
Full Changelog: v0.6.2...v0.6.3