AlexsLemonade scpca-nf issues

AlexsLemonade / 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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issues

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Prune SingleR results?

#803 jashapiro opened 5 days ago
0
Set minimum and maximum cutoffs for mitochondrial content filtering

#802 jashapiro opened 1 week ago
1
Add minimum number of cells (3) for merge

#801 jashapiro closed 2 weeks ago
1
Merge changes from #799 into main

#800 jashapiro closed 3 weeks ago
0
Increase minimum cells to 3

#799 jashapiro closed 3 weeks ago
0
[BUG] PCA not created when n_cells = 2

#798 jashapiro closed 3 weeks ago
3
Merge main into dev

#797 jashapiro closed 3 weeks ago
0
Merge development into main

#796 jashapiro closed 3 weeks ago
0
Use scpcatools 0.4.1 images

#795 jashapiro closed 3 weeks ago
0
convert addParams to take

#794 jashapiro closed 3 weeks ago
0
Prepare for scpca-nf release `v0.8.5`

#793 jashapiro closed 3 weeks ago
1
Use scpcaTools 0.4.1 images

#792 jashapiro closed 3 weeks ago
1
remove `addParams`

#791 jashapiro closed 3 weeks ago
1
[BUG] Counts on portal are not integers as expected

#790 jashapiro closed 3 weeks ago
0
[BUG] Error in h5ad conversion with Singularity(?)

#789 jashapiro opened 1 month ago
2
[pre-commit.ci] pre-commit autoupdate

#788 pre-commit-ci[bot] closed 4 weeks ago
0
Merge Development into Main

#787 jashapiro closed 3 months ago
0
Update version numbers

#786 jashapiro closed 3 months ago
0
Prepare for scpca-nf release `v0.8.4`

#785 jashapiro closed 3 months ago
1
Merged HVGS into `main`

#784 allyhawkins closed 3 months ago
0
Account for different HVG name in merged object

#783 allyhawkins closed 3 months ago
0
Actually sync changes for counting libraries into `main`

#782 allyhawkins closed 3 months ago
0
Sync change to counting libraries

#781 allyhawkins closed 3 months ago
0
Only count single cell libraries for max merged

#780 allyhawkins closed 3 months ago
0
Sync changes from `development` into `main` for v0.8.3

#779 allyhawkins closed 3 months ago
0
Update versions and bug fix for v0.8.3

#778 allyhawkins closed 3 months ago
0
Add parameter for maximum number of libraries to allow when merging

#777 allyhawkins closed 3 months ago
1
Skip creating merged objects if there are too many samples

#776 allyhawkins closed 3 months ago
1
Prepare for scpca-nf release `v0.8.3`

#775 allyhawkins closed 3 months ago
0
Improve scanpy compatibility

#774 jashapiro closed 3 months ago
1
Update AnnData output for improved scanpy compatibility

#773 jashapiro closed 3 months ago
2
Sync changes from `development` into `main`

#772 allyhawkins closed 4 months ago
0
Change version to v0.8.2

#771 allyhawkins closed 4 months ago
1
Prepare for scpca-nf release `v0.8.2`

#770 allyhawkins closed 4 months ago
4
Add sample metadata tables to reports

#769 allyhawkins closed 4 months ago
3
[pre-commit.ci] pre-commit autoupdate

#768 pre-commit-ci[bot] closed 4 months ago
1
Move bulk output to separate bulk directory

#767 allyhawkins closed 5 months ago
0
Output bulk data to a `bulk` folder rather than individual files within project directory

#766 allyhawkins closed 5 months ago
1
Add sample metadata table to QC and cell type reports

#765 allyhawkins closed 4 months ago
5
Re-order bulk metadata to match order for overall sample metadata

#764 allyhawkins closed 5 months ago
1
Test new docker image and add test samples to profile config

#763 allyhawkins closed 6 months ago
3
Use new, slimmer sometimes, containers

#762 jashapiro closed 6 months ago
0
Test use of smaller Docker images in workflow

#761 allyhawkins closed 5 months ago
1
Use new smaller images in processes

#760 jashapiro closed 6 months ago
1
Delete duplicate layer in AnnData objects

#759 jashapiro closed 6 months ago
0
Consider using nf-schema plugin to validate inputs

#758 jashapiro opened 6 months ago
0
Fix some merge bugs

#757 allyhawkins closed 6 months ago
1
Define umap point size when creating cell type umaps

#756 allyhawkins closed 7 months ago
1
Fix bugs for dealing with processed objects with only 1 cell

#755 allyhawkins closed 7 months ago
3
Sync changes from `main` with `dev`

#754 allyhawkins closed 7 months ago
0