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AlexsLemonade
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scpca-nf
scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data
BSD 3-Clause "New" or "Revised" License
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Merge Development into Main
#787
jashapiro
closed
1 month ago
0
Update version numbers
#786
jashapiro
closed
1 month ago
0
Prepare for scpca-nf release `v0.8.4`
#785
jashapiro
closed
1 month ago
1
Merged HVGS into `main`
#784
allyhawkins
closed
1 month ago
0
Account for different HVG name in merged object
#783
allyhawkins
closed
1 month ago
0
Actually sync changes for counting libraries into `main`
#782
allyhawkins
closed
1 month ago
0
Sync change to counting libraries
#781
allyhawkins
closed
1 month ago
0
Only count single cell libraries for max merged
#780
allyhawkins
closed
1 month ago
0
Sync changes from `development` into `main` for v0.8.3
#779
allyhawkins
closed
1 month ago
0
Update versions and bug fix for v0.8.3
#778
allyhawkins
closed
1 month ago
0
Add parameter for maximum number of libraries to allow when merging
#777
allyhawkins
closed
1 month ago
1
Skip creating merged objects if there are too many samples
#776
allyhawkins
closed
1 month ago
1
Prepare for scpca-nf release `v0.8.3`
#775
allyhawkins
closed
1 month ago
0
Improve scanpy compatibility
#774
jashapiro
closed
1 month ago
1
Update AnnData output for improved scanpy compatibility
#773
jashapiro
closed
1 month ago
2
Sync changes from `development` into `main`
#772
allyhawkins
closed
2 months ago
0
Change version to v0.8.2
#771
allyhawkins
closed
2 months ago
1
Prepare for scpca-nf release `v0.8.2`
#770
allyhawkins
closed
2 months ago
4
Add sample metadata tables to reports
#769
allyhawkins
closed
2 months ago
3
[pre-commit.ci] pre-commit autoupdate
#768
pre-commit-ci[bot]
closed
2 months ago
1
Move bulk output to separate bulk directory
#767
allyhawkins
closed
2 months ago
0
Output bulk data to a `bulk` folder rather than individual files within project directory
#766
allyhawkins
closed
2 months ago
1
Add sample metadata table to QC and cell type reports
#765
allyhawkins
closed
2 months ago
5
Re-order bulk metadata to match order for overall sample metadata
#764
allyhawkins
closed
2 months ago
1
Test new docker image and add test samples to profile config
#763
allyhawkins
closed
3 months ago
3
Use new, slimmer sometimes, containers
#762
jashapiro
closed
3 months ago
0
Test use of smaller Docker images in workflow
#761
allyhawkins
closed
3 months ago
1
Use new smaller images in processes
#760
jashapiro
closed
3 months ago
1
Delete duplicate layer in AnnData objects
#759
jashapiro
closed
4 months ago
0
Consider using nf-schema plugin to validate inputs
#758
jashapiro
opened
4 months ago
0
Fix some merge bugs
#757
allyhawkins
closed
4 months ago
1
Define umap point size when creating cell type umaps
#756
allyhawkins
closed
4 months ago
1
Fix bugs for dealing with processed objects with only 1 cell
#755
allyhawkins
closed
4 months ago
3
Sync changes from `main` with `dev`
#754
allyhawkins
closed
4 months ago
0
Fix bugs with generating example data
#753
allyhawkins
closed
4 months ago
0
Sync changes from `development` with removal of merge conflicts
#752
allyhawkins
closed
4 months ago
1
Sync changes from `main` into `development`
#751
allyhawkins
closed
4 months ago
1
Sync `development` into `main`
#750
allyhawkins
closed
4 months ago
1
Update tags to v0.8.1
#749
allyhawkins
closed
4 months ago
0
Prepare for scpca-nf release `v0.8.1`
#748
allyhawkins
closed
4 months ago
0
Use more specialized docker images for processes
#747
jashapiro
closed
3 months ago
2
Test workflow with Bioc3.19 images
#746
jashapiro
closed
3 months ago
1
Account for no cells being assigned to a sample when demultiplexing
#745
allyhawkins
closed
5 months ago
0
Account for .h5ad in output feature file
#744
allyhawkins
closed
5 months ago
0
Skip CellAssign if only 1 cell
#743
allyhawkins
closed
5 months ago
0
Account for demultiplexing without genetic demultiplexing
#742
allyhawkins
closed
5 months ago
1
`project_celltype_metafile` parameter is missing from scpca-nf schema
#741
sjspielman
opened
5 months ago
0
[BUG] Account for grabbing estimated demux cell counts for libraries with no genetic demultiplexing
#740
allyhawkins
closed
5 months ago
1
Make example ids consistent
#739
sjspielman
closed
5 months ago
0
Skip processing if no cells remain after empty droplet filtering
#738
allyhawkins
closed
5 months ago
1
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