Metadata-Version: 2.1
Name: bcl2fq-local
Version: 0.2.0
Summary: Bcl2fastq wrapper
Home-page: https://github.com/seahurt/bcl2fq-local
Author: Wang Jianghao
Author-email: haozi.vv@gmail.com
License: MIT
Description: # bcl2fq-local
        
        A bcl2fastq and qc wrapper
        
        # Install
        ```bash
        pip install bcl2fq-local
        ```
        or 
        
        ```bash
        git clone URL
        cd bcl2fq-local
        python setup.py install
        
        ```
        
        # Usage
        For Bcl2fastq
        ```text
        usage: bcl2fq-local [-h] [-i DirPath] [-o DirPath] [--sample-sheet File]
                            [--mismatch N] [--process N] [--io-process Num]
                            [--binpath File] [--dry-run] [--mask MASK]
                            [--mask-reads N] [--mask-index N] [-v]
        
        A bcl2fastq wrapper
        
        optional arguments:
          -h, --help           show this help message and exit
          -i DirPath           Sequence run dir
          -o DirPath           Output dir for fastq files
          --sample-sheet File  Using custom sample sheet file
          --mismatch N         Mismatch for barcode, default: 1
          --process N          Process number for demultiplexing and processing
          --io-process Num     Process number for reading and writing
          --binpath File       bcl2fastq binary file path
          --dry-run            Only print the cmd without running it
          --mask MASK          using self defined mask
          --mask-reads N       set reads mask base count, default is: 0,0
          --mask-index N       set index mask base count, default is: 0,0
          -v, --version        show version info
        ```
        
        For QC
        ```text
        usage: qc-local [-h] [-r RAW_DIR] [-c CLEAN_DIR] [-q QC_DIR] [-2 ADAPTER_DIR]
                        [-t THREADS] [--paired-end] [-v]
        
        A qc wrapper
        
        optional arguments:
          -h, --help      show this help message and exit
          -r RAW_DIR      Raw reads dir input
          -c CLEAN_DIR    Dir to write output clean reads
          -q QC_DIR       Dir to write qc info file, default: <clean_dir>/QC
          -2 ADAPTER_DIR  Dir to write removed reads, default: <clean_dir>/002
          -t THREADS      Threads number for parallel, default:8
          --paired-end    Use qc for paired end reads
          -v, --version   Show version info
        ```
        
        
Platform: CentOS 7.0+
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: System Administrators
Classifier: Operating System :: POSIX :: Linux
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Description-Content-Type: text/markdown
