AlexsLemonade/scpca-nf

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scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data

Stars: 18
Forks: 2
Open beginner issues: 0
Indexed issues: 48
Avg merge: 4h 21m
Merged PRs (30d): 12

Dominant language: R
License: BSD-3-Clause
Last GitHub push: Sep 1, 2026
Latest indexed: Sep 14, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

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48 open issues indexed

Implement fenced divs to make a two-column html output. Open

QC

AlexsLemonade/scpca-nf#508 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Improve aesthetics of QC report Open

QC

AlexsLemonade/scpca-nf#507 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add sample count checks to genetic demultiplexing Open

AlexsLemonade/scpca-nf#100 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Check metadata fields as part of the workflow Open

AlexsLemonade/scpca-nf#127 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[BUG] missing rad files? Open

bug

AlexsLemonade/scpca-nf#213 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Test script for downloading reference files and containers Open

AlexsLemonade/scpca-nf#234 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Include parameter for specifying integration order in integration workflow Open

AlexsLemonade/scpca-nf#275 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Future issue: Modify integration workflow to incorporate additional covariates for harmony Open

AlexsLemonade/scpca-nf#278 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Expand documentation on contents of repository Open

AlexsLemonade/scpca-nf#285 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Support converting to AnnData objects with multiplexed libraries Open

AlexsLemonade/scpca-nf#424 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Use submitter ontology labels, if provided Open

AlexsLemonade/scpca-nf#559 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Update merged report UMAP sizing Open

QC

AlexsLemonade/scpca-nf#641 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Check for missing bulk in genetic demux Open

AlexsLemonade/scpca-nf#674 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Add troubleshooting section to external instructions Open

AlexsLemonade/scpca-nf#690 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Include instructions for specifying `merge_run_ids` when merging projects in external instructions Open

nice to have

AlexsLemonade/scpca-nf#715 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Future idea: Create merged objects for projects with multiplexed libraries containing all non-multiplexed single-cell libraries Open

AlexsLemonade/scpca-nf#718 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Consider using nf-schema plugin to validate inputs Open

AlexsLemonade/scpca-nf#758 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Set minimum and maximum cutoffs for mitochondrial content filtering Open

AlexsLemonade/scpca-nf#802 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Prune SingleR results? Open

AlexsLemonade/scpca-nf#803 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add a reference for zebrafish as a model organism Open

AlexsLemonade/scpca-nf#812 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add bam options to Space Ranger? Open

AlexsLemonade/scpca-nf#828 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Create Docker images on cavatica Open

AlexsLemonade/scpca-nf#859 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add GHA to file an issue to create a cavatica release when a new version is tagged Open

AlexsLemonade/scpca-nf#894 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Future idea: Update handling for SingleR references Open

AlexsLemonade/scpca-nf#906 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Create workflow to build Docker images tagged by version Open

AlexsLemonade/scpca-nf#997 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Future thought: Combine reference cells for different diagnoses in multiplexed libraries Open

AlexsLemonade/scpca-nf#1098 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Only show changes > 0.00% in the metrics report Open

AlexsLemonade/scpca-nf#1115 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Check for removed or modified input files throughout Open

AlexsLemonade/scpca-nf#1142 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Limit number of marker genes in QC report Open

AlexsLemonade/scpca-nf#1157 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Allow "merge" of single sample projects (or at least skip them) Open

AlexsLemonade/scpca-nf#1179 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Automate updates to sb_nextflow_schema.yaml Open

AlexsLemonade/scpca-nf#1198 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Consider retaining spatial symlinks Open

AlexsLemonade/scpca-nf#1223 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Expand spatial outputs Open

AlexsLemonade/scpca-nf#1224 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Allow for other probes when building cell type references Open

AlexsLemonade/scpca-nf#1247 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Update example metadata to be strictly examples Open

AlexsLemonade/scpca-nf#1251 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add new profile for workflow testing data Open

AlexsLemonade/scpca-nf#1252 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Plan for cell typing mouse samples Open

AlexsLemonade/scpca-nf#1262 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Update parsing line for new flex probe versions Open

AlexsLemonade/scpca-nf#1263 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Consider updating workflow when there are too few cells for celltyping Open

AlexsLemonade/scpca-nf#1265 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Be more permissive with file name checks Open

AlexsLemonade/scpca-nf#1267 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[BUG] _metrics.json is missing alevin-fry version info Open

bug

AlexsLemonade/scpca-nf#1269 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add GPU support for CellAssign Open

AlexsLemonade/scpca-nf#1270 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[BUG] file() called with null arg Open

bug

AlexsLemonade/scpca-nf#1273 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Make compatible with strict syntax Open

AlexsLemonade/scpca-nf#1279 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Discussion: Tie checkpoints to releases Open

AlexsLemonade/scpca-nf#1325 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Update how the sample type is defined Open

AlexsLemonade/scpca-nf#1332 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Prepare for scpca-nf release `v0.10.6` Open

AlexsLemonade/scpca-nf#1346 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Handle higher memory needs for CellAssign Open

AlexsLemonade/scpca-nf#1347 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

AlexsLemonade/scpca-nf

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