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nf-core/sourmash/gather @ 0.0.0-6c4ed3a

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 sketch signature kmer containment sourmash genomics metagenomics taxonomic classification taxonomic profiling
Latest version: 0.0.0-6c4ed3a
Total downloads: 13
Source: nf-core/modules
Authors: @vmikk @taylorreiter
Maintainers: @vmikk @taylorreiter

Summary

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.

Get started

Add the following snippet to your workflow script to include this module.

include { SOURMASH_GATHER } from 'nf-core/sourmash/gather'

License

MIT License

Process
Name SOURMASH_GATHER
Input 6 channels
#1 tuple
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 6 channels
#1 result tuple
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}
#2 matches tuple
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}
#3 prefetch tuple
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}
#4 unassigned tuple
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}
#5 prefetchcsv tuple
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}
#6 versions_sourmash tuple
${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
Tool Description Homepage
sourmash Compute and compare FracMinHash signatures for DNA data sets. https://sourmash.readthedocs.io/
Version 0.0.0-6c4ed3a
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 23 Apr 2026 15:46:58 (UTC)