Compress fastq with spring
Project description
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>
.
-
Recursively find all fastq pairs
-
Compress all pairs with spring
file_1.fastq + file_2.fastq (spring)-> file.spring
-
Decompress with spring
file.spring (spring)-> file_1.fastq + file_2.fastq
-
Compare checksum with previous
file_1.fastq + file_2.fastq (hashlib)-> compare
-
Delete fastq (If the compression was lossless)
file_1.fastq + file_2.fastq (rm)->
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