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`
`:map`

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

`signatures`
`:file`

Files containing signature (hash sketches) of reference genomes

*.{sig}

`ksize`
`:integer`

ksize value

Output

name:type

description

pattern

`signature_index`

`meta`
`:map`

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

`*.sbt.zip`
`:file`

Database of signatures

*.{sbt.zip}

`versions_sourmash`

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

The name of the process

`sourmash`
`:string`

The name of the tool

`sourmash --version 2>&1 | sed 's/^sourmash //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`sourmash`
`:string`

The name of the tool

`sourmash --version 2>&1 | sed 's/^sourmash //'`
`:eval`

The expression to obtain the version of the tool

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`
`:map`

`signatures`
`:file`

`ksize`
`:integer`

Output

`signature_index`

`meta`
`:map`

`*.sbt.zip`
`:file`

`versions_sourmash`

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

`sourmash`
`:string`

`sourmash --version 2>&1 | sed 's/^sourmash //'`
`:eval`

Topics

`versions`

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

`sourmash`
`:string`

`sourmash --version 2>&1 | sed 's/^sourmash //'`
`:eval`

Tools

sourmash
BSD-3-clause

included in

maintainer

get in touch

modules/sourmash_index

Description

Input

meta :map

signatures :file

ksize :integer

Output

signature_index

meta :map

*.sbt.zip :file

versions_sourmash

${task.process} :string

sourmash :string

sourmash --version 2>&1 | sed 's/^sourmash //' :eval

Topics

versions

${task.process} :string

sourmash :string

sourmash --version 2>&1 | sed 's/^sourmash //' :eval

Tools

sourmashBSD-3-clause

included in

maintainer

get in touch

`meta`
`:map`

`signatures`
`:file`

`ksize`
`:integer`

`signature_index`

`meta`
`:map`

`*.sbt.zip`
`:file`

`versions_sourmash`

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

`sourmash`
`:string`

`sourmash --version 2>&1 | sed 's/^sourmash //'`
`:eval`

`versions`

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

`sourmash`
`:string`

`sourmash --version 2>&1 | sed 's/^sourmash //'`
`:eval`

sourmash
BSD-3-clause