cruise-toolkit 1.0.0

Unified CLI wrapper for barcode/UMI & CR/UR tools

cruise-toolkit

cruise-toolkit is a unified Python toolkit that integrates barcode splitting, CB/UMI correction, counting, and CR/UR alignment steps commonly used in single-cell and spatial transcriptomics pipelines.

It provides a single command-line entry point — cruise-toolkit — wrapping your original cruise.py workflow script, while preserving argument compatibility.

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🔧 Installation

From source (development mode):

git clone https://github.com/dawangran/cruise-toolkit.git
cd cruise-toolkit
pip install -e .

In the future, installation from PyPI will be supported:

pip install cruise-toolkit

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🚀 Quick Start

Run the main workflow (arguments are fully compatible with your original cruise.py script):

cruise-toolkit \
  --bam input.bam \
  --fastqs fq1.fastq.gz,fq2.fastq.gz \
  --valid-cell valid.cell.tsv \
  --adapt ATGCGCGATAACCTC \
  --model BBBBBBBBBBATGBBBBBBBBBBATGUUUUUUUUUUTTTT \
  --threads 16 \
  --cb-tags CC,CB \
  --umi-tag UB \
  --outdir cruise_out

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🖥️ CLI Usage

Show help:

cruise-toolkit -h
cruise-toolkit --help

This will display the native arguments of cruise.py, including --bam, --fastqs, --adapt, --model, --cb-tags, --umi-tag, etc.

Global options (apply to all runs):

• --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
  Set global logging level (default: INFO)
• --log-file run.log
  Save logs to file
• --version
  Show version

Example:

cruise-toolkit --log-level DEBUG --log-file run.log \
  --bam input.bam --fastqs fq1.fq.gz,fq2.fq.gz --outdir cruise_out

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📜 Common Arguments

Argument	Description
--bam	Input BAM file
--fastqs	Comma-separated list of FASTQ files
--valid-cell	File with valid cell barcodes
--adapt	Adapter sequence
--model	CB/UMI model string
--threads	Number of threads
--cb-tags	Cell barcode tags (e.g., CC,CB)
--umi-tag	UMI tag (e.g., UB)
--outdir	Output directory
--keep-sample-tmp / --no-keep-sample-tmp	Whether to keep intermediate files

All argument definitions remain identical to the original cruise.py.
Use cruise-toolkit --help to view the full parameter list.

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📝 Logging System

All runs can be configured with global logging options:

cruise-toolkit --log-level INFO --log-file pipeline.log \
  --bam input.bam --fastqs fq1.fq.gz,fq2.fq.gz ...

Logs are printed to stderr and optionally written to a file.

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🧪 Development & Testing

# Install dev dependencies
pip install -e .[dev]

# Run tests
pytest -q

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👤 Author

• Dawn

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📄 License

MIT License