bedtools/bedtools_sort
sort
BED
GFF
VCF
Description
Sorts a feature file (bed/gff/vcf) by chromosome and other criteria.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input file (bed/gff/vcf) to be sorted. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o | file output | Output sorted file (bed/gff/vcf) to be written. |
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. |
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 v0.3.1 \
-main-script target/nextflow/bedtools/bedtools_sort/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
bedtools/bedtools_sortbiobox v0.3.1
Uses
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