mapseq2biom
Description¶
Process MAPseq output into biom and krona-txt formats
Pipelines¶
This module is used by the following pipelines:
Installation¶
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install mapseq2biom
Tools¶
mapseq2biom¶
Process MAPseq output into biom and krona-txt formats, uses mgnify-pipelines-toolkit as conda environment
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] |
- |
msq |
file | MAPseq output file | *.mseq |
db_otu |
file | Processed reference database otu file | *.otu |
db_label |
string | Reference database label | - |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] |
- |
krona_input |
file | Converted .txt file to be used with Krona | *.txt |
biom_out |
file | Converted biom file | *.tsv |
biom_notaxid_out |
file | Converted biom file without taxids | *.tsv |
versions |
file | File containing software versions | versions.yml |
