modules/nucmer

NUCmer is a pipeline for the alignment of multiple closely related nucleotide sequences.

alignnucleotidesequence

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

Description

NUCmer is a pipeline for the alignment of multiple closely related nucleotide sequences.

Input

name:type

description

pattern

`meta`
`:map`

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

`ref`
`:file`

FASTA file of the reference sequence

*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}

`query`
`:file`

FASTA file of the query sequence

*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}

Output

name:type

description

pattern

`delta`

`meta`
`:map`

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

`*.delta`
`:file`

File containing coordinates of matches between reference and query

`coords`

`meta`
`:map`

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

`*.coords`
`:file`

NUCmer1.1 coords output file

*.{coords}

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

nucmer
The Artistic License

NUCmer is a pipeline for the alignment of multiple closely related nucleotide sequences.

http://mummer.sourceforge.net 10.1186/gb-2004-5-2-r12

modules/nucmer

Description

Input

`meta`
`:map`

`ref`
`:file`

`query`
`:file`

Output

`delta`

`meta`
`:map`

`*.delta`
`:file`

`coords`

`meta`
`:map`

`*.coords`
`:file`

`versions`

`versions.yml`
`:file`

Tools

nucmer
The Artistic License

maintainers

get in touch

modules/nucmer

Description

Input

meta:map

ref:file

query:file

Output

delta

meta:map

*.delta:file

coords

meta:map

*.coords:file

versions

versions.yml:file

Tools

nucmer The Artistic License

maintainers

get in touch

`meta`
`:map`

`ref`
`:file`

`query`
`:file`

`delta`

`meta`
`:map`

`*.delta`
`:file`

`coords`

`meta`
`:map`

`*.coords`
`:file`

`versions`

`versions.yml`
`:file`

nucmer
The Artistic License