modules/mudskipper_index

Build and store a gtf index, which is useful for converting genomic BAM/SAM files to transcriptomic BAM/SAM files.

bamtranscriptometranscriptomicindexmudskippersam

https://github.com/nf-core/modules/[...]/modules/nf-core/mudskipper/index

Description

Build and store a gtf index, which is useful for converting genomic BAM/SAM files to transcriptomic BAM/SAM files.

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing annotation information e.g. [ id:'genome' ]

`gtf`
`:file`

Transcript annotation file.

*.{gtf,gff,gff3}

Output

name:type

description

pattern

`index`

`meta`
`:map`

Groovy Map containing annotation information e.g. [ id:'genome' ]

`${prefix}/`
`:directory`

Mudskipper index for running mudskipper conversion tools

${prefix}/

`versions_mudskipper`

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

The name of the process

`mudskipper`
`:string`

The name of the tool

`mudskipper -V 2>&1 | sed 's/.*mudskipper //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`mudskipper`
`:string`

The name of the tool

`mudskipper -V 2>&1 | sed 's/.*mudskipper //'`
`:eval`

The expression to obtain the version of the tool

Tools

mudskipper
BSD 3-clause

mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic BAM/RAD files.

github.com/OceanGenomics/mudskipper

modules/mudskipper_index

Description

Input

`meta`
`:map`

`gtf`
`:file`

Output

`index`

`meta`
`:map`

`${prefix}/`
`:directory`

`versions_mudskipper`

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

`mudskipper`
`:string`

`mudskipper -V 2>&1 | sed 's/.*mudskipper //'`
`:eval`

Topics

`versions`

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

`mudskipper`
`:string`

`mudskipper -V 2>&1 | sed 's/.*mudskipper //'`
`:eval`

Tools

mudskipper
BSD 3-clause

maintainer

get in touch

modules/mudskipper_index

Description

Input

meta :map

gtf :file

Output

index

meta :map

${prefix}/ :directory

versions_mudskipper

${task.process} :string

mudskipper :string

mudskipper -V 2>&1 | sed 's/.*mudskipper //' :eval

Topics

versions

${task.process} :string

mudskipper :string

mudskipper -V 2>&1 | sed 's/.*mudskipper //' :eval

Tools

mudskipperBSD 3-clause

maintainer

get in touch

`meta`
`:map`

`gtf`
`:file`

`index`

`meta`
`:map`

`${prefix}/`
`:directory`

`versions_mudskipper`

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

`mudskipper`
`:string`

`mudskipper -V 2>&1 | sed 's/.*mudskipper //'`
`:eval`

`versions`

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

`mudskipper`
`:string`

`mudskipper -V 2>&1 | sed 's/.*mudskipper //'`
`:eval`

mudskipper
BSD 3-clause