Description

igv.js is an embeddable interactive genome visualization component

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

alignment:file

Sorted BAM/CRAM file

*.{bam,cram}

index:file

Index of sorted BAM/CRAM file

*.{bai,crai}

Output

name:type
description
pattern

browser

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*_genome-browser.html:file

Genome browser HTML file

*.{html}

align_files

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

alignment:file

Copy of the input sorted BAM/CRAM file

*.{bam,cram}

index_files

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

index:file

Copy of the input index of sorted BAM/CRAM file

*.{bai,crai}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

igv
MIT

Create an embeddable interactive genome browser component. Output files are expected to be present in the same directory as the genome browser html file. To visualise it, files have to be served. Check the documentation at: https://github.com/igvteam/igv-webapp for an example and https://github.com/igvteam/igv.js/wiki/Data-Server-Requirements for server requirements

github.com/igvteam/igv.js github.com/igvteam/igv.js/wiki https://github.com/igvteam/igv.js 10.1093/bioinformatics/btac830
maintainer
Github user mirpedrol
get in touch
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