bgzip

Description

Block compression/decompression utility

Type

bash_script

License

MIT

Links

Repository

Documentation

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output"  
index_name: "$id.$key.index_name"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/toolbox.git \  
  -revision v0.1.1 \  
  -main-script target/nextflow/bgzip/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	file to be compressed or decompressed

Name

Type & Properties

--input

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	compressed or decompressed output
--index_name -I	file output	name of BGZF index file [file.gz.gzi]

Name

Type & Properties

--output

file

required

output

--index_name

-I

file

output

Arguments

Name	Type & Properties	Description
--offset -b	integer	decompress at virtual file pointer (0-based uncompressed offset)
--decompress -d	boolean_true	decompress the input file
--rebgzip -g	boolean_true	use an index file to bgzip a file
--index -i	boolean_true	compress and create BGZF index
--compress_level -l	integer	compression level to use when compressing; 0 to 9, or -1 for default [-1]
--reindex -r	boolean_true	(re)index the output file
--size -s	integer	decompress INT bytes (uncompressed size)
--test -t	boolean_true	test integrity of compressed file
--binary	boolean_true	Don't align blocks with text lines

Name

Type & Properties

--offset

-b

integer

--decompress

-d

boolean_true

--rebgzip

-g

boolean_true

--index

-i

boolean_true

--compress_level

-l

integer

--reindex

-r

boolean_true

--size

-s

integer

--test

-t

boolean_true

--binary

boolean_true