Nextflow Registry | nf-core/metamaps/classify@0.0.0-6c4ed3a

nf-core/metamaps/classify @ 0.0.0-6c4ed3a

Strain-level metagenomic assignment

metamaps long reads metagenomics taxonomy

Latest version: 0.0.0-6c4ed3a

Total downloads: 11

Source: nf-core/modules

Authors: @henningonsbring @sofstam

Strain-level metagenomic assignment

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

include { METAMAPS_CLASSIFY } from 'nf-core/metamaps/classify'

MIT License

Process

`Name`	`METAMAPS_CLASSIFY`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`classification_res` file	Coordinates where reads map `*.{classification_res}`
`meta_file` file	Statistics for mapping result `*.{classification_res.meta}`
`meta_unmappedreadsLengths` file	Statistics for length of unmapped reads `*.{classification_res.meta.unmappedReadsLengths}`
`para_file` file	Log with parameters `*.{classification_res.parameters}`

`database_folder` directory	Path to MetaMaps database `*`

Output 8 channels

#1 em tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*classification_res.EM` file	The final and complete set of approximate read mappings `*.{classification_res.EM}`

#2 wimp tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*classification_res.EM.WIMP` file	Sample composition at different taxonomic levels `*.{classification_res.EM.WIMP}`

#3 krona tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*classification_res.EM.reads2Taxon.krona` file	Taxon ID assignment of reads in Krona format `*.{classification_res.EM.reads2Taxon.krona}`

#4 versions

`versions.yml` file	File containing software versions `versions.yml`

#5 reads2taxon tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*classification_res.EM.reads2Taxon` file	Taxon ID assignment of reads `*.{classification_res.EM.reads2Taxon}`

#6 length_and_id tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*classification_res.EM.lengthAndIdentitiesPerMappingUnit` file	Read length and estimated identity for all reads `*.{classification_res.EM.lengthAndIdentitiesPerMappingUnit}`

#7 contig_coverage tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*classification_res.EM.contigCoverage` file	Read coverage for contigs `*.{classification_res.EM.contigCoverage}`

#8 evidence_unknown_species tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*classification_res.EM.evidenceUnknownSpecies` file	Statistics on read identities and zero-coverage regions `*.{classification_res.EM.evidenceUnknownSpecies}`

Tool	Description	Homepage
metamaps	MetaMaps is a tool for long-read metagenomic analysis	https://github.com/DiltheyLab/MetaMaps