mapseq_otu_krona

Description

Taxononmy assignment and visualisation of reads using input reference database

Installation

ebi-metagenomics/mapseq_otu_krona

nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install mapseq_otu_krona

Keywords: taxonomy, rRNA, MAPseq, krona

Components

This subworkflow uses the following components:

• mapseq (module)
• mapseq2biom (module)
• krona/ktimporttext (module)

Input

Name	Type	Description	Pattern
ch_fasta	file	The input channel containing the FASTA file containing reads Structure: [ val(meta), path(fasta) ]	*.{fasta/fasta.gz}
ch_dbs	tuple	A structured tuple containing the different reference database files Some of these files are processed specifically for use by MAPseq Structure: [ path(fasta), path(tax), path(otu), path(mscluster), val(label) ]	-

Output

Name	Type	Description	Pattern
mseq	file	MAPseq output file Structure: [ val(meta), path(mseq) ]	*.mseq
krona_input	file	mapseq2biom output file to be used as input to Krona Structure: [ val(meta), path(txt) ]	*.txt
biom_out	file	mapseq2biom output Biom file Structure: [ val(meta), path(tsv) ]	*.tsv
biom_notaxid_out	file	mapseq2biom output Biom file without taxids Structure: [ val(meta), path(tsv) ]	*.tsv
html	file	Krona output html file Structure: [ val(meta), path(html) ]	*.html
versions	file	File containing software versions Structure: [ path(versions.yml) ]	versions.yml

People

Authors

• @chrisata

Maintainers

• @chrisata