bedtools/bedtools_links
Links
BED
GFF
VCF
Description
Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a file.
This is useful for cases when one wants to manually inspect through a large set of annotations or features.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input file (bed/gff/vcf). |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o | file output | Output HTML file to be written. |
Options
Name | Type & Properties | Description |
|---|---|---|
--base_url -base | string | The “basename” for the UCSC browser. |
--organism -org | string | The organism (e.g. mouse, human). |
--database -db | string | The genome build. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output"
base_url: [ "http://genome.ucsc.edu" ]
organism: [ "human" ]
database: [ "hg18" ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/biobox.git \
-revision v0.3.0 \
-main-script target/nextflow/bedtools/bedtools_links/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
bedtools/bedtools_linksbiobox v0.3.0
Uses
0 relationships
No component dependencies found.