amr_annotation
Description¶
AMR annotation, harmonisation and integration
Installation¶
ebi-metagenomics/amr_annotation
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install amr_annotation
Components¶
This subworkflow uses the following components:
deeparg/downloaddata(module)deeparg/predict(module)hamronization/deeparg(module)rgi/cardannotation(module)rgi/main(module)hamronization/rgi(module)amrfinderplus/update(module)amrfinderplus/run(module)amrintegrator(module)rgi/downloaddb(module)
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] |
- |
ch_inputs |
file | The input channel containing the protein fasta file and gff file e.g. [ [meta], aminoacids, cds_gff ] |
- |
ch_amrfinderplus_db |
file | The input channel containing the path to the compressed amrfinderplus database | *.tar.gz |
ch_deeparg_db |
file | The input channel containing the path to deeparg database | - |
ch_deeparg_db_version |
value | The input channel containing the database version of deeparg | [0-9] |
ch_deeparg_model |
value | The input channel containing the deeparg model SS for reads or LS for genes/proteins | SS or LS |
ch_deeparg_tool_version |
value | The input channel containing the deeparg tool version | [0-9].[0-9].[0-9] |
ch_rgi_db |
file | The input channel containing the path to the CARD database properly formatted for RGI | - |
skip_amrfinderplus |
boolean | skip amrfinderplus (true) or run it (false) | true or false |
skip_deeparg |
boolean | skip deeparg (true) or run it (false) | true or false |
skip_rgi |
boolean | skip rgi (true) or run it (false) | true or false |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
versions |
file | File containing software versions Structure: [ path(versions.yml) ] | versions.yml |
gff |
Channel containing a gff file with ARG annotation Structure: [ val(meta), path("*.gff") ] | - |
