modules/sourmash_taxannotate

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

fracminhash sketchsignaturekmercontainmentsourmashgenomicsmetagenomicstaxonomic classificationtaxonomic profiling

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

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`

`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_taxannotate

Description

Input

meta:map

gather_results:file

taxonomy:file

Output

result

meta:map

*.with-lineages.csv.gz:file

versions

versions.yml:file

Tools

sourmash BSD-3-clause

`meta:map`

`gather_results:file`

`taxonomy:file`

`result`

`meta:map`

`*.with-lineages.csv.gz:file`

`versions`

`versions.yml:file`

sourmash
BSD-3-clause