modules/sourmash_gather

Search a metagenome sourmash signature against one or many reference databases and return the minimum set of genomes that contain the k-mers in the metagenome.

FracMinHash sketchsignaturekmercontainmentsourmashgenomicsmetagenomicstaxonomic classificationtaxonomic profiling

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

Description

Search a metagenome sourmash signature against one or many reference databases and return the minimum set of genomes that contain the k-mers in the metagenome.

Input

name:type

description

pattern

`meta`
`:map`

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

`signature`
`:file`

File containing signatures (hash sketches) of a sample

*.{sig}

`database`
`:file`

database

`save_unassigned`
`:boolean`

If true, output will contain a file that is a sourmash signature containing the unassigned hashes from the query

`save_matches_sig`
`:boolean`

If true, output will contain a file that is a sourmash signature composed of the FracMinHash sketches that were matched in the database and that matched the query

`save_prefetch`
`:boolean`

If true, output will contain a file with all prefetch-matched signatures from the database

`save_prefetch_csv`
`:boolean`

If true, output will contain a csv file with the names of all prefetch-matched signatures

Output

name:type

description

pattern

`result`

`meta`
`:map`

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

`*.csv.gz`
`:file`

Table with signatures classified as belonging to any of the genomes in the sourmash database(s).

*{csv.gz}

`unassigned`

`meta`
`:map`

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

`*_unassigned.sig.zip`
`:file`

A FracMinHash sketch containing hashes (k-mers) that did not match to any of the genomes in the sourmash database(s).

*{sig.zip}

`matches`

`meta`
`:map`

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

`*_matches.sig.zip`
`:file`

A signature containing FracMinHash sketches of genomes in the sourmash database.

*{sig.zip}

`prefetch`

`meta`
`:map`

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

`*_prefetch.sig.zip`
`:file`

All prefetch-matched signatures from the database.

*{sig.zip}

`prefetchcsv`

`meta`
`:map`

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

`*_prefetch.csv.gz`
`:file`

The names of all prefetch-matched signatures from the database in CSV format.

*{csv.gz}

`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_gather

Description

Input

`meta`
`:map`

`signature`
`:file`

`database`
`:file`

`save_unassigned`
`:boolean`

`save_matches_sig`
`:boolean`

`save_prefetch`
`:boolean`

`save_prefetch_csv`
`:boolean`

Output

`result`

`meta`
`:map`

`*.csv.gz`
`:file`

`unassigned`

`meta`
`:map`

`*_unassigned.sig.zip`
`:file`

`matches`

`meta`
`:map`

`*_matches.sig.zip`
`:file`

`prefetch`

`meta`
`:map`

`*_prefetch.sig.zip`
`:file`

`prefetchcsv`

`meta`
`:map`

`*_prefetch.csv.gz`
`: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

maintainers

get in touch

modules/sourmash_gather

Description

Input

meta:map

signature:file

database:file

save_unassigned:boolean

save_matches_sig:boolean

save_prefetch:boolean

save_prefetch_csv:boolean

Output

result

meta:map

*.csv.gz:file

unassigned

meta:map

*_unassigned.sig.zip:file

matches

meta:map

*_matches.sig.zip:file

prefetch

meta:map

*_prefetch.sig.zip:file

prefetchcsv

meta:map

*_prefetch.csv.gz: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

maintainers

get in touch

`meta`
`:map`

`signature`
`:file`

`database`
`:file`

`save_unassigned`
`:boolean`

`save_matches_sig`
`:boolean`

`save_prefetch`
`:boolean`

`save_prefetch_csv`
`:boolean`

`result`

`meta`
`:map`

`*.csv.gz`
`:file`

`unassigned`

`meta`
`:map`

`*_unassigned.sig.zip`
`:file`

`matches`

`meta`
`:map`

`*_matches.sig.zip`
`:file`

`prefetch`

`meta`
`:map`

`*_prefetch.sig.zip`
`:file`

`prefetchcsv`

`meta`
`:map`

`*_prefetch.csv.gz`
`: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