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

]

`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

]

`*.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

]

`*_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

]

`*_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

]

`*_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

]

`*_prefetch.csv.gz:file`

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

*{csv.gz}

`versions`

`versions.yml: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_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`

`versions.yml:file`

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

versions.yml:file

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`

`versions.yml:file`

sourmash
BSD-3-clause