fq/fq_lint

fastq

lint

validate

quality-control

Description

Validates a single or paired FASTQ file.

Type

bash_script

License

MIT

Keywords

fastq

lint

validate

quality-control

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
lint_mode: [ "panic" ]  
single_read_validation_level: [ "high" ]  
paired_read_validation_level: [ "high" ]  
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_lint/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--input_1	file required	Read 1 source. Accepts both raw and gzipped FASTQ inputs.
--input_2	file	Read 2 source. Accepts both raw and gzipped FASTQ inputs.

Name

Type & Properties

--input_1

file

required

--input_2

file

Options

Name	Type & Properties	Description
--lint_mode	string	Panic on first error or log all errors.
--single_read_validation_level	string	Only use single read validators up to a given level.
--paired_read_validation_level	string	Only use paired read validators up to a given level.
--disable_validator	string multiple	Disable validators by code. Use multiple times to disable more than one.
--record_definition_separator	string	Define a record definition separator.

Name

Type & Properties

--lint_mode

string

--single_read_validation_level

string

--paired_read_validation_level

string

--disable_validator

string

multiple

--record_definition_separator

string