modules/sourmash_index

Create a database of sourmash signatures (a group of FracMinHash sketches) to be used as references.

signaturessourmashgenomicsmetagenomicsmappingkmer

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

Description

Create a database of sourmash signatures (a group of FracMinHash sketches) to be used as references.

Input

name:type

description

pattern

`meta{:bash}`
`:map`

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

`signatures{:bash}`
`:file`

Files containing signature (hash sketches) of reference genomes

*.{sig}

`ksize{:bash}`
`:integer`

ksize value

Output

name:type

description

pattern

`signature_index{:bash}`

`meta{:bash}`
`:map`

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

`*.sbt.zip{:bash}`
`:file`

Database of signatures

*.{sbt.zip}

`versions{:bash}`

`versions.yml{:bash}`
`:file`

File containing software versions

versions.yml

Tools

sourmash
BSD-3-clause

Compute and compare FracMinHash signatures for DNA data sets.

sourmash.readthedocs.io https://github.com/sourmash-bio/sourmash 10.21105/joss.00027

modules/sourmash_index

Description

Input

`meta{:bash}`
`:map`

`signatures{:bash}`
`:file`

`ksize{:bash}`
`:integer`

Output

`signature_index{:bash}`

`meta{:bash}`
`:map`

`*.sbt.zip{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

Tools

sourmash
BSD-3-clause

included in

maintainer

get in touch

modules/sourmash_index

Description

Input

meta{:bash}:map

signatures{:bash}:file

ksize{:bash}:integer

Output

signature_index{:bash}

meta{:bash}:map

*.sbt.zip{:bash}:file

versions{:bash}

versions.yml{:bash}:file

Tools

sourmash BSD-3-clause

included in

maintainer

get in touch

`meta{:bash}`
`:map`

`signatures{:bash}`
`:file`

`ksize{:bash}`
`:integer`

`signature_index{:bash}`

`meta{:bash}`
`:map`

`*.sbt.zip{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

sourmash
BSD-3-clause