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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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Change Anndata extension to h5ad
#737
jashapiro
closed
5 months ago
0
Discussion: Rename AnnData objects with .h5ad extension
#736
jashapiro
closed
4 months ago
6
[BUG] Age in sample_metadata is inconsistently typed
#735
jashapiro
closed
4 months ago
3
Reduce merge memory a touch
#734
jashapiro
closed
5 months ago
6
[pre-commit.ci] pre-commit autoupdate
#733
pre-commit-ci[bot]
closed
3 months ago
1
[pre-commit.ci] pre-commit autoupdate
#732
pre-commit-ci[bot]
closed
5 months ago
0
Make sure CellAssign is skipped for any objects with just 1 cell
#731
allyhawkins
closed
4 months ago
1
Fix bugs in v0.8.0
#730
allyhawkins
closed
6 months ago
0
[pre-commit.ci] pre-commit autoupdate
#729
pre-commit-ci[bot]
closed
6 months ago
0
Sync changes from `development` with `main` for v0.8.0
#728
allyhawkins
closed
6 months ago
0
Update version tag and scpcaTools container
#727
allyhawkins
closed
6 months ago
1
Use `mem_max` for all merging and sync changes from `main`
#726
allyhawkins
closed
6 months ago
0
Handle empty sample type columns and add sentence about references not having tumor cells
#725
allyhawkins
closed
6 months ago
1
v0.7.3
#724
allyhawkins
closed
6 months ago
0
Prepare for scpca-nf release v0.7.3
#723
allyhawkins
closed
6 months ago
0
Add max_mem label for Cell Assign
#722
allyhawkins
closed
6 months ago
0
Update overview figure
#721
allyhawkins
closed
6 months ago
0
Add nextflow_schema.json file
#720
jashapiro
closed
6 months ago
2
Skip merging projects with multiplexed libraries
#719
allyhawkins
closed
6 months ago
1
Future idea: Create merged objects for projects with multiplexed libraries containing all non-multiplexed single-cell libraries
#718
allyhawkins
opened
6 months ago
0
Fix column name typos
#717
sjspielman
closed
6 months ago
4
Skip creation of merged objects
#716
allyhawkins
closed
6 months ago
1
Include instructions for specifying `merge_run_ids` when merging projects in external instructions
#715
allyhawkins
opened
6 months ago
0
Create nextflow_schema.json file
#714
jashapiro
closed
6 months ago
1
Add is_xenograft & is_cell_line to example metadata
#713
sjspielman
closed
6 months ago
6
Reduce SCE file sizes
#712
jashapiro
closed
6 months ago
0
Bump memory for CCDL only
#711
jashapiro
closed
6 months ago
0
Ideas for reducing file sizes
#710
jashapiro
closed
6 months ago
6
[BUG] CellAssign process getting killed with `OutOfMemoryError`
#709
allyhawkins
closed
6 months ago
10
Specify merging only specific runs from a project
#708
allyhawkins
closed
6 months ago
0
Add sentence to cell type report indicating references come from normal samples
#707
allyhawkins
closed
6 months ago
2
Update merge publishDir
#706
sjspielman
closed
6 months ago
1
Specify run ids to use when merging projects
#705
allyhawkins
closed
6 months ago
1
Discussion: Should we change the merged publish directory to be the given project directory?
#704
sjspielman
closed
6 months ago
4
Add CI to contributing
#703
sjspielman
closed
6 months ago
0
Restore heatmap legend
#702
sjspielman
closed
6 months ago
1
Add missing legend to celltype report
#701
sjspielman
closed
6 months ago
1
[pre-commit.ci] pre-commit autoupdate
#700
pre-commit-ci[bot]
closed
6 months ago
1
Fix multiplex anndata export
#699
sjspielman
closed
6 months ago
1
Ensure merge workflow exports AnnData for multiplexed samples
#698
sjspielman
closed
6 months ago
2
Fix merge report bugs related to multiplexing
#697
sjspielman
closed
6 months ago
0
Skip any additional processing to processed objects with 0 cells
#696
allyhawkins
closed
6 months ago
2
Add precommit ci to CONTRIBUTING.md
#695
sjspielman
closed
6 months ago
2
add autofix setting & update
#694
jashapiro
closed
7 months ago
3
add some pre-commit.ci options
#693
jashapiro
closed
7 months ago
0
Add docs for custom cell type references
#692
sjspielman
closed
7 months ago
2
Standardize celltype report filenames
#691
arkid15r
closed
7 months ago
1
Add troubleshooting section to external instructions
#690
sjspielman
opened
7 months ago
3
QC report aesthetic updates
#689
sjspielman
closed
7 months ago
1
Add merge.nf external instructions
#688
sjspielman
closed
7 months ago
7
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