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
Pipelines¶
This subworkflow is used by the following pipelines:
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 |
