modules/mash_screen

Screens query sequences against large sequence databases

screencontainmentcontaminationtaxonomic assignment

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

Description

Screens query sequences against large sequence databases

Input

name:type

description

pattern

`meta`
`:map`

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

`query`
`:file`

Query sequences

*.fastq.gz

`meta2`
`:map`

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

`sequences_sketch`
`:file`

sketch file of sequences

Output

name:type

description

pattern

`screen`

`meta`
`:map`

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

`*.screen`
`:file`

List of sequences from fastx_db similar to query sequences

*.screen

`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_screen

Description

Input

`meta`
`:map`

`query`
`:file`

`meta2`
`:map`

`sequences_sketch`
`:file`

Output

`screen`

`meta`
`:map`

`*.screen`
`: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_screen

Description

Input

meta :map

query :file

meta2 :map

sequences_sketch :file

Output

screen

meta :map

*.screen :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`

`meta2`
`:map`

`sequences_sketch`
`:file`

`screen`

`meta`
`:map`

`*.screen`
`: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