Description

Module that calls normalize-by-median.py from khmer. The module can take a mix of paired end (interleaved) and single end reads. If both types are provided, only a single file with single ends is possible.

Input

name:type
description
pattern

meta

:map

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

fastq_paired

:file

Paired-end interleaved fastq files

*.{fq,fastq}.gz

fastq_unpaired

:file

Single-end fastq files

*.{fq,fastq}.gz

Output

name:type
description
pattern

reads

meta

:map

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

*.fastq.gz

:file

Interleaved fastq files

*.{fq,fastq}.gz

versions_khmer

${task.process}

:string

The process the versions were collected from

khmer

:string

The name of the tool

normalize-by-median.py --version 2>&1 | grep ^khmer | sed "s/^khmer //"

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The process the versions were collected from

khmer

:string

The name of the tool

normalize-by-median.py --version 2>&1 | grep ^khmer | sed "s/^khmer //"

:eval

The expression to obtain the version of the tool

Tools

maintainer
Github user erikrikarddaniel
get in touch
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