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+++ b/0.6.1/modules/abricate/run/README.md	Tue Sep 05 11:51:40 2023 -0400
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+# NextFlow DSL2 Module
+
+```bash
+ABRICATE_RUN
+```
+
+## Description
+
+Run `abricate` tool on a list of assembled contigs in FASTA format given a list of database names. Produces a single output table in ASCII text format per database.
+
+\
+ 
+
+### `input:`
+
+___
+
+Type: `tuple`
+
+Takes in the following tuple of metadata (`meta`) and a list of assemled contig FASTA files of input type `path` (`assembly`).
+
+Ex:
+
+```groovy
+[ [id: 'sample1', single_end: true], '/data/sample1/f_assembly.fa' ]
+```
+
+\
+ 
+
+#### `meta`
+
+Type: Groovy Map
+
+A Groovy Map containing the metadata about the FASTQ file.
+
+Ex:
+
+```groovy
+[ id: 'FAL00870', strandedness: 'unstranded', single_end: true ]
+```
+
+\
+ 
+
+#### `assembly`
+
+Type: `path`
+
+NextFlow input type of `path` pointing to assembled contig file in FASTA format.
+
+\
+ 
+
+#### `abdbs`
+
+Type: `val`
+
+Nextflow input type of `val` containing a list of at least one of the following database names on which `abricate` should be run.
+
+Ex:
+
+```groovy
+[ 'resfinder', 'megares', 'ncbi', 'ncbiamrplus', 'argannot' , 'ecoli_vf' ]
+```
+
+\
+ 
+
+### `output:`
+
+___
+
+Type: `tuple`
+
+Outputs a tuple of metadata (`meta` from `input:`) and list of `abricate` result files (`abricated`).
+
+\
+ 
+
+#### `abricated`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `abricate` results table file per sample (`id:`).
+
+\
+ 
+
+#### `versions`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.