bedtools/bedtools_sort

sort

BED

GFF

VCF

Description

Sorts a feature file (bed/gff/vcf) by chromosome and other criteria.

Type

bash_script

License

GPL-2.0, MIT

Keywords

sort

BED

GFF

VCF

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 v0.2.0 \  
  -main-script target/nextflow/bedtools/bedtools_sort/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Input file (bed/gff/vcf) to be sorted.

Name

Type & Properties

--input

-i

file

required

Outputs

Name	Type & Properties	Description
--output -o	file output	Output sorted file (bed/gff/vcf) to be written.

Name

Type & Properties

--output

-o

file

output

Options

Name	Type & Properties	Description
--sizeA	boolean_true	Sort by feature size in ascending order.
--sizeD	boolean_true	Sort by feature size in descending order.
--chrThenSizeA	boolean_true	Sort by chrom (asc), then feature size (asc).
--chrThenSizeD	boolean_true	Sort by chrom (asc), then feature size (desc).
--chrThenScoreA	boolean_true	Sort by chrom (asc), then score (asc).
--chrThenScoreD	boolean_true	Sort by chrom (asc), then score (desc).
--genome -g	file	Sort according to the chromosomes declared in "genome.txt"
--faidx	file	Sort according to the chromosomes declared in "names.txt"
--header	boolean_true	Print the header from the A file prior to results.

Name

Type & Properties

--sizeA

boolean_true

--sizeD

boolean_true

--chrThenSizeA

boolean_true

--chrThenSizeD

boolean_true

--chrThenScoreA

boolean_true

--chrThenScoreD

boolean_true

--genome

-g

file

--faidx

file

--header

boolean_true