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`

`versions.yml`
`:file`

File containing software versions

versions.yml

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`

`versions.yml`
`:file`

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

versions.yml:file

Tools

khmer BSD 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`

`versions.yml`
`:file`

khmer
BSD License