modules/ucsc_gtftogenepred

compute average score of bigwig over bed file

gtfgenepredrefflatucscgtftogenepred

https://github.com/nf-core/modules/[...]/modules/nf-core/ucsc/gtftogenepred

Description

compute average score of bigwig over bed file

Input

name:type

description

pattern

`meta:map`

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

]

`gtf:file`

GTF file

*.{gtf}

Output

name:type

description

pattern

`genepred`

`meta:map`

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

]

`*.genepred:file`

genepred file

*.{genepred}

`refflat`

`meta:map`

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

]

`*.refflat:file`

refflat file

*.{refflat}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

ucsc
varies; see http://genome.ucsc.edu/license

Convert GTF files to GenePred format

http://hgdownload.cse.ucsc.edu/admin/exe

modules/ucsc_gtftogenepred

Description

Input

meta:map

gtf:file

Output

genepred

meta:map

*.genepred:file

refflat

meta:map

*.refflat:file

versions

versions.yml:file

Tools

ucsc varies; see http://genome.ucsc.edu/license

`meta:map`

`gtf:file`

`genepred`

`meta:map`

`*.genepred:file`

`refflat`

`meta:map`

`*.refflat:file`

`versions`

`versions.yml:file`

ucsc
varies; see http://genome.ucsc.edu/license