modules/bbmap_bbnorm

BBNorm is designed to normalize coverage by down-sampling reads over high-depth areas of a genome, to result in a flat coverage distribution.

normalizationassemblycoverage

https://github.com/nf-core/modules/[...]/modules/nf-core/bbmap/bbnorm

Description

BBNorm is designed to normalize coverage by down-sampling reads over high-depth areas of a genome, to result in a flat coverage distribution.

Input

name:type

description

pattern

`meta`
`:map`

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

`fastq`
`:file`

fastq file

*.{fastq,fq}(.gz)?

Output

name:type

description

pattern

`fastq`

`meta`
`:map`

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

`*.fastq.gz`
`:file`

fastq file

*.{fastq, fq}.gz

`log`

`meta`
`:map`

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

`*.log`
`:file`

log file

*.log

`versions_bbmap`

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

The name of the process

`bbmap`
`:string`

The name of the tool

`bbversion.sh | grep -v "Duplicate cpuset"`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`bbmap`
`:string`

The name of the tool

`bbversion.sh | grep -v "Duplicate cpuset"`
`:eval`

The expression to obtain the version of the tool

Tools

bbmap
BBMap - Bushnell B. - sourceforge.net/projects/bbmap/

BBMap is a short read aligner, as well as various other bioinformatic tools.

jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbnorm-guide/

modules/bbmap_bbnorm

Description

Input

`meta`
`:map`

`fastq`
`:file`

Output

`fastq`

`meta`
`:map`

`*.fastq.gz`
`:file`

`log`

`meta`
`:map`

`*.log`
`:file`

`versions_bbmap`

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

`bbmap`
`:string`

`bbversion.sh | grep -v "Duplicate cpuset"`
`:eval`

Topics

`versions`

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

`bbmap`
`:string`

`bbversion.sh | grep -v "Duplicate cpuset"`
`:eval`

Tools

bbmap
BBMap - Bushnell B. - sourceforge.net/projects/bbmap/

included in

maintainer

get in touch

modules/bbmap_bbnorm

Description

Input

meta:map

fastq:file

Output

fastq

meta:map

*.fastq.gz:file

log

meta:map

*.log:file

versions_bbmap

${task.process}:string

bbmap:string

bbversion.sh | grep -v "Duplicate cpuset":eval

Topics

versions

${task.process}:string

bbmap:string

bbversion.sh | grep -v "Duplicate cpuset":eval

Tools

bbmap BBMap - Bushnell B. - sourceforge.net/projects/bbmap/

included in

maintainer

get in touch

`meta`
`:map`

`fastq`
`:file`

`fastq`

`meta`
`:map`

`*.fastq.gz`
`:file`

`log`

`meta`
`:map`

`*.log`
`:file`

`versions_bbmap`

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

`bbmap`
`:string`

`bbversion.sh | grep -v "Duplicate cpuset"`
`:eval`

`versions`

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

`bbmap`
`:string`

`bbversion.sh | grep -v "Duplicate cpuset"`
`:eval`

bbmap
BBMap - Bushnell B. - sourceforge.net/projects/bbmap/