bedtools/bedtools_expand

genomics

intervals

expand

split

comma-separated

replicate

Description

Expand rows by splitting comma-separated values into separate rows.

This tool replicates lines based on columns containing comma-separated values,
creating one row for each value. Useful for expanding collapsed data formats
like BED12 blocks or multi-value annotations into individual entries.

Type

bash_script

License

MIT

Keywords

genomics

intervals

expand

split

comma-separated

replicate

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.bed"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.1 \  
  -main-script target/nextflow/bedtools/bedtools_expand/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Input file with comma-separated values to expand. Format: Tab-delimited file with one or more columns containing comma-separated values Example: BED file with comma-separated scores or annotations

Name

Type & Properties

--input

-i

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Output file with expanded rows. Contains one row for each comma-separated value, with other columns replicated across all expanded rows.

Name

Type & Properties

--output

file

required

output

Expansion Options

Name	Type & Properties	Description
--columns -c	string required	Column(s) to expand (1-based indexing). Single column: Specify one column number (e.g., "4") Multiple columns: Comma-separated list (e.g., "4,5") Behavior: Values in specified columns are split and expanded Requirement: All specified columns must have same number of values

Name

Type & Properties

--columns

-c

string

required