modules/igv_js

igv.js is an embeddable interactive genome visualization component

igvigv.jsjsgenome browser

https://github.com/nf-core/modules/[...]/modules/nf-core/igv/js

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_cat`

`${task.process}`
`:string`

The name of the process

`cat`
`:string`

The name of the tool

`cat --version |& sed '1!d;s/.*coreutils) //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`cat`
`:string`

The name of the tool

`cat --version |& sed '1!d;s/.*coreutils) //'`
`:eval`

The expression to obtain the version of the tool

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

modules/igv_js

Description

Input

`meta`
`:map`

`alignment`
`:file`

`index`
`:file`

Output

`browser`

`meta`
`:map`

`*_genome-browser.html`
`:file`

`align_files`

`meta`
`:map`

`alignment`
`:file`

`index_files`

`meta`
`:map`

`index`
`:file`

`versions_cat`

`${task.process}`
`:string`

`cat`
`:string`

`cat --version |& sed '1!d;s/.*coreutils) //'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`cat`
`:string`

`cat --version |& sed '1!d;s/.*coreutils) //'`
`:eval`

Tools

igv
MIT

maintainer

get in touch

modules/igv_js

Description

Input

meta :map

alignment :file

index :file

Output

browser

meta :map

*_genome-browser.html :file

align_files

meta :map

alignment :file

index_files

meta :map

index :file

versions_cat

${task.process} :string

cat :string

cat --version |& sed '1!d;s/.*coreutils) //' :eval

Topics

versions

${task.process} :string

cat :string

cat --version |& sed '1!d;s/.*coreutils) //' :eval

Tools

igvMIT

maintainer

get in touch

`meta`
`:map`

`alignment`
`:file`

`index`
`:file`

`browser`

`meta`
`:map`

`*_genome-browser.html`
`:file`

`align_files`

`meta`
`:map`

`alignment`
`:file`

`index_files`

`meta`
`:map`

`index`
`:file`

`versions_cat`

`${task.process}`
`:string`

`cat`
`:string`

`cat --version |& sed '1!d;s/.*coreutils) //'`
`:eval`

`versions`

`${task.process}`
`:string`

`cat`
`:string`

`cat --version |& sed '1!d;s/.*coreutils) //'`
`:eval`

igv
MIT