fq/fq_subsample

fastq

subsample

subset

Description

fq subsample outputs a subset of records from single or paired FASTQ files.

Type

bash_script

License

MIT

Keywords

fastq

subsample

subset

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output_1: "$id.$key.output_1"  
output_2: "$id.$key.output_2"  
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_subsample/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--input_1	file required	First input fastq file to subsample. Accepts both raw and gzipped FASTQ inputs.
--input_2	file	Second input fastq files to subsample. Accepts both raw and gzipped FASTQ inputs.

Name

Type & Properties

--input_1

file

required

--input_2

file

Output

Name	Type & Properties	Description
--output_1	file output	Sampled read 1 fastq files. Output will be gzipped if ends in `.gz`.
--output_2	file output	Sampled read 2 fastq files. Output will be gzipped if ends in `.gz`.

Name

Type & Properties

--output_1

file

output

--output_2

file

output

Options

Name	Type & Properties	Description
--probability	double	The probability a record is kept, as a percentage (0.0, 1.0). Cannot be used with `record-count`
--record_count	integer	The exact number of records to keep. Cannot be used with `probability`
--seed	integer	Seed to use for the random number generator

Name

Type & Properties

--probability

double

--record_count

integer

--seed

integer