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Unified Wrapper - #20

Merged

Claptar merged 36 commits into

mainfrom

dev

Feb 18, 2026

Merged

Unified Wrapper#20
Claptar merged 36 commits into
mainfrom
dev

Commits on Jun 5, 2025
- Modularised starsolo script
  Claptar
  committed
  e6768bf
Commits on Jun 6, 2025
- Fixed output directory path and removed for loops in gzipping
  Claptar
  committed
  b1f48ab
- Returned original path to reference and whitelists
  Claptar
  committed
  58c3141
- Add usage note for species in main function
  Claptar
  committed
  13f0270
- Refactor starsolo_10x_auto.sh for improved readability and functionality
  Claptar
  committed
  62c8902
Commits on Feb 17, 2026
- Add starsolo script for unified CLI scRNA-seq processing
  cellgeni
  committed
  dd72aa2
- Add default configuration file for STARsolo CLI
  cellgeni
  committed
  6b63199
- Add platform-specific scripts for various sequencing technologies
  cellgeni
  committed
  b752b60
- Add STARsolo wrapper scripts for various sequencing methods and a QC script
  cellgeni
  committed
  da0455f
- Add install script for STARsolo CLI to facilitate command setup
  cellgeni
  committed
  c05e07e
- Update README.md to enhance clarity on `starsolo` CLI usage and supported platforms
  cellgeni
  committed
  3a33eab
- Add check to ensure main function runs only when script is executed directly
  cellgeni
  committed
  e6bd6c3
- Add script to generate synthetic dataset for STARsolo CLI wrapper
  cellgeni
  committed
  7e7bd8a
Commits on Feb 18, 2026
- Add test dataset archive for STARsolo data validation
  cellgeni
  committed
  74e7cb4
- Add whitelists archive
  cellgeni
  committed
  6fa511b
- Add GitHub Actions workflow for automated testing of STARsolo
  cellgeni
  committed
  9ceb015
- added fails-fast option
  Claptar
  committed
  e211604
- Refactor GitHub Actions workflow to improve test data unpacking and remove fails-fast option
  Claptar
  committed
  f368126
- Refactor platform scripts to convert paths to absolute before changing directories
  Claptar
  committed
  63fdf93
- Simplify test data unpacking step in GitHub Actions workflow
  Claptar
  committed
  aa52d0d
- Ensure fail-fast option is set to false in test workflow strategy
  Claptar
  committed
  181a2eb
- Refactor test step to handle smartseq technology input conditionally
  Claptar
  committed
  43370c3
- Refactor run_smartseq function to convert manifest paths to absolute before writing to output directory
  Claptar
  committed
  cb9a15e
- Remove temporary manifest file after processing in run_smartseq function
  Claptar
  committed
  8949779
- Refactor test step to streamline smartseq input handling and remove redundant variables
  Claptar
  committed
  0fea315
- Debugging this stuff
  Claptar
  committed
  8de1024
- Update test data archive to reflect recent changes
  Claptar
  committed
  c1b4782
- Update Dockerfile to use latest versions of samtools and seqtk, and streamline installation process
  Claptar
  committed
  6ff4236
- Add GitHub Actions workflow for building and pushing Docker image on tag creation
  Claptar
  committed
  fac6b6e
- Update test workflow to ignore additional paths on push events
  Claptar
  committed
  06246e7
- Update Dockerfile to install pbzip2 and adjust WORKDIR for CLI execution
  Claptar
  committed
  f4967da
- Refactor Dockerfile to use base image and streamline installation process
  Claptar
  committed
  4661a2b
- Update test workflow to use the correct Docker container for testing
  Claptar
  committed
  2a3609e
- Update Docker build workflow to specify cache-from and cache-to for improved performance
  Claptar
  committed
  ad7e559
- Fallback
  Claptar
  committed
  d23076a
- Refactor run_10x function to convert paths to absolute and streamline output directory creation
  Claptar
  committed
  633ce4d

Commits

Commits on Jun 5, 2025

Commits on Jun 6, 2025

Commits on Feb 17, 2026

Commits on Feb 18, 2026