modules/adapterremovalfixprefix

Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup.

adapterremovalfastqdedup

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

Description

Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup.

Input

name:type

description

pattern

`meta`
`:map`

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

`fastq`
`:file`

FASTQ file from AdapterRemoval2

*.{fq.gz,fastq.gz}

Output

name:type

description

pattern

`fixed_fastq`

`meta`
`:map`

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

`*.fq.gz`
`:file`

FASTQ file with fixed read prefixes for DeDup

*.{fq.gz}

`versions_adapterremovalfixprefix`

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

The name of the process

`adapterremovalfixprefix`
`:string`

The name of the tool

`echo 0.0.5`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`adapterremovalfixprefix`
`:string`

The name of the tool

`echo 0.0.5`
`:eval`

The expression to obtain the version of the tool

Tools

adapterremovalfixprefix
GPL v3

Fixes adapter removal prefixes to make sure no clashing read names are in the output.

github.com/apeltzer/AdapterRemovalFixPrefix https://github.com/apeltzer/AdapterRemovalFixPrefix 10.1186/s13059-016-0918-z

modules/adapterremovalfixprefix

Description

Input

`meta`
`:map`

`fastq`
`:file`

Output

`fixed_fastq`

`meta`
`:map`

`*.fq.gz`
`:file`

`versions_adapterremovalfixprefix`

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

`adapterremovalfixprefix`
`:string`

`echo 0.0.5`
`:eval`

Topics

`versions`

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

`adapterremovalfixprefix`
`:string`

`echo 0.0.5`
`:eval`

Tools

adapterremovalfixprefix
GPL v3

maintainer

get in touch

modules/adapterremovalfixprefix

Description

Input

meta:map

fastq:file

Output

fixed_fastq

meta:map

*.fq.gz:file

versions_adapterremovalfixprefix

${task.process}:string

adapterremovalfixprefix:string

echo 0.0.5:eval

Topics

versions

${task.process}:string

adapterremovalfixprefix:string

echo 0.0.5:eval

Tools

adapterremovalfixprefix GPL v3

maintainer

get in touch

`meta`
`:map`

`fastq`
`:file`

`fixed_fastq`

`meta`
`:map`

`*.fq.gz`
`:file`

`versions_adapterremovalfixprefix`

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

`adapterremovalfixprefix`
`:string`

`echo 0.0.5`
`:eval`

`versions`

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

`adapterremovalfixprefix`
`:string`

`echo 0.0.5`
`:eval`

adapterremovalfixprefix
GPL v3