crunchy 0.1

Compress fastq with spring

Crunchy

A python wrapper around spring to compress fastq and check the integrity.

Install

git clone https://github.com/Clinical-Genomics/crunchy
pip install -e .
crunchy --help
Usage: crunchy [OPTIONS] COMMAND [ARGS]...

  Base command for crunchy

Options:
  --spring-binary TEXT            Path to spring binary  [default: spring]
  -t, --threads INTEGER           Number of threads to use for spring
                                  compression  [default: 8]
  --log-level [DEBUG|INFO|WARNING]
                                  Choose what log messages to show
  --help                          Show this message and exit.

Commands:
  auto        Recursively find all fastq pairs below a directory and spring...
  checksum    Create a checksum for the file(s)
  compress    Compress a file
  decompress  Decompress a file

Workflow

Each command can be run separately. To compress all fastq pairs below a directory run crunchy auto <path_to_dir>.

1. Recursively find all fastq pairs

2. Compress all pairs with spring file_1.fastq + file_2.fastq (spring)-> file.spring

3. Decompress with spring file.spring (spring)-> file_1.fastq + file_2.fastq

4. Compare checksum with previous file_1.fastq + file_2.fastq (hashlib)-> compare

5. Delete fastq (If the compression was lossless) file_1.fastq + file_2.fastq (rm)->