bcl2fq-local 0.2.0

Description:

bcl2fqlocal 0.2.0

bcl2fq-local
A bcl2fastq and qc wrapper
Install
pip install bcl2fq-local

or
git clone URL
cd bcl2fq-local
python setup.py install

Usage
For Bcl2fastq
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
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