modules/khmer_uniquekmers

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

khmerk-mereffective genome size

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

Description

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`fasta`
`:file`

fasta file

*.{fa,fasta}

`kmer_size`
`:integer`

k-mer size to use

Output

name:type

description

pattern

`report`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.report.txt`
`:file`

Text file containing unique-kmers.py execution report

*.report.txt

`kmers`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.kmers.txt`
`:file`

Text file containing number of kmers

*.kmers.txt

`versions_khmer`

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

The process the versions were collected from

`khmer`
`:string`

The name of the tool

`unique-kmers.py --version 2>&1 | grep ^khmer | sed "s/^khmer //;s/ .*$//"`
`: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

`unique-kmers.py --version 2>&1 | grep ^khmer | sed "s/^khmer //;s/ .*$//"`
`:eval`

The expression to obtain the version of the tool

Tools

khmer
BSD License

khmer k-mer counting library

github.com/dib-lab/khmer khmer.readthedocs.io/en/latest https://github.com/dib-lab/khmer 10.12688/f1000research.6924.1

modules/khmer_uniquekmers

Description

Input

`meta`
`:map`

`fasta`
`:file`

`kmer_size`
`:integer`

Output

`report`

`meta`
`:map`

`*.report.txt`
`:file`

`kmers`

`meta`
`:map`

`*.kmers.txt`
`:file`

`versions_khmer`

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

`khmer`
`:string`

`unique-kmers.py --version 2>&1 | grep ^khmer | sed "s/^khmer //;s/ .*$//"`
`:eval`

Topics

`versions`

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

`khmer`
`:string`

`unique-kmers.py --version 2>&1 | grep ^khmer | sed "s/^khmer //;s/ .*$//"`
`:eval`

Tools

khmer
BSD License

included in

maintainer

get in touch

modules/khmer_uniquekmers

Description

Input

meta :map

fasta :file

kmer_size :integer

Output

report

meta :map

*.report.txt :file

kmers

meta :map

*.kmers.txt :file

versions_khmer

${task.process} :string

khmer :string

unique-kmers.py --version 2>&1 | grep ^khmer | sed "s/^khmer //;s/ .*$//" :eval

Topics

versions

${task.process} :string

khmer :string

unique-kmers.py --version 2>&1 | grep ^khmer | sed "s/^khmer //;s/ .*$//" :eval

Tools

khmerBSD License

included in

maintainer

get in touch

`meta`
`:map`

`fasta`
`:file`

`kmer_size`
`:integer`

`report`

`meta`
`:map`

`*.report.txt`
`:file`

`kmers`

`meta`
`:map`

`*.kmers.txt`
`:file`

`versions_khmer`

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

`khmer`
`:string`

`unique-kmers.py --version 2>&1 | grep ^khmer | sed "s/^khmer //;s/ .*$//"`
`:eval`

`versions`

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

`khmer`
`:string`

`unique-kmers.py --version 2>&1 | grep ^khmer | sed "s/^khmer //;s/ .*$//"`
`:eval`

khmer
BSD License