fq/fq_filter

fastq

filter

sequence

Description

Filters a FASTQ file based on record names or sequence patterns.

Type

bash_script

License

MIT

Keywords

fastq

filter

sequence

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

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

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.0 \  
  -main-script target/nextflow/fq/fq_filter/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--input	file required	FASTQ source file. Accepts both raw and gzipped FASTQ inputs.

Name

Type & Properties

--input

file

required

Output

Name	Type & Properties	Description
--output	file required output	Filtered FASTQ destination file. Output will be gzipped if ends in `.gz`.

Name

Type & Properties

--output

file

required

output

Options

Name	Type & Properties	Description
--names	file	File containing allowlist of record names (one per line).
--sequence_pattern	string	Keep records that have sequences that match the given regular expression.

Name

Type & Properties

--names

file

--sequence_pattern

string