amrintegrator
Description¶
Module that integrates the outputs of ARG annotation tools into a single GFF file
Installation¶
ebi-metagenomics/amrintegrator
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install amrintegrator
Tools¶
amrintegrator¶
Integrates the standardised output of deeparg, rgi, and amrfinderplus into a single gff file, uses mgnify-pipelines-toolkit as conda environment
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'sample1' ] |
- |
deeparg |
file | Tab-delimited file of DEEPARG result after hAMRonization | *.tsv |
rgi |
file | Tab-delimited file of RGI result after hAMRonization | *.tsv |
amrfp |
file | Tab-delimited file of AMRfinderPlus result after hAMRonization | *.tsv |
gff |
file | The GFF3 file corresponding to the annotated genes and proteins. It could be gz compressed | *.{gff,gff.gz} |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
gff |
file | - | |
versions |
file | - |
