modules/mash_dist

Calculate Mash distances between reference and query sequences

distanceestimatereferencequery

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

Description

Calculate Mash distances between reference and query sequences

Input

name:type

description

pattern

`meta`
`:map`

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

`query`
`:file`

FASTA, FASTQ or Mash sketch

*.{fasta,fasta.gz,fastq,fastq.gz,msh}

`reference`
`:file`

FASTA, FASTQ or Mash sketch

*.{fasta,fasta.gz,fastq,fastq.gz,msh}

Output

name:type

description

pattern

`dist`

`meta`
`:map`

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

`*.txt`
`:file`

The results from mash dist

*.txt

`versions_mash`

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

The name of the process

`mash`
`:string`

The name of the tool

`mash --version 2>&1`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`mash`
`:string`

The name of the tool

`mash --version 2>&1`
`:eval`

The expression to obtain the version of the tool

Tools

mash
https://github.com/marbl/Mash/blob/master/LICENSE.txt

Fast sequence distance estimator that uses MinHash

github.com/marbl/Mash mash.readthedocs.io/en/latest/sketches https://github.com/marbl/Mash 10.1186/s13059-016-0997-x

modules/mash_dist

Description

Input

`meta`
`:map`

`query`
`:file`

`reference`
`:file`

Output

`dist`

`meta`
`:map`

`*.txt`
`:file`

`versions_mash`

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

`mash`
`:string`

`mash --version 2>&1`
`:eval`

Topics

`versions`

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

`mash`
`:string`

`mash --version 2>&1`
`:eval`

Tools

mash
https://github.com/marbl/Mash/blob/master/LICENSE.txt

included in

maintainer

get in touch

modules/mash_dist

Description

Input

meta :map

query :file

reference :file

Output

dist

meta :map

*.txt :file

versions_mash

${task.process} :string

mash :string

mash --version 2>&1 :eval

Topics

versions

${task.process} :string

mash :string

mash --version 2>&1 :eval

Tools

mashhttps://github.com/marbl/Mash/blob/master/LICENSE.txt

included in

maintainer

get in touch

`meta`
`:map`

`query`
`:file`

`reference`
`:file`

`dist`

`meta`
`:map`

`*.txt`
`:file`

`versions_mash`

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

`mash`
`:string`

`mash --version 2>&1`
`:eval`

`versions`

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

`mash`
`:string`

`mash --version 2>&1`
`:eval`

mash
https://github.com/marbl/Mash/blob/master/LICENSE.txt