Description

Annotate list of metagenome members (based on sourmash signature matches) with taxonomic information.

Input

name:type
description
pattern

meta

:map

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

gather_results

:file

Mandatory table with signatures classified as belonging to any of the genomes in the sourmash database(s), result of sourmash gather command.

taxonomy

:file

One or more databases with lineages (in CSV format, Mandatory)

Output

name:type
description
pattern

result

meta

:map

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

*.with-lineages.csv.gz

:file

Table with signatures classified as belonging to any of the genomes in the sourmash database(s) with an additional ‘lineage’ column containing the taxonomic information for each database match.

*{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
maintainers
Github user vmikk
Github user taylorreiter
get in touch
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