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+++ b/0.2.1/modules/amrfinderplus/run/README.md	Mon Jun 27 15:55:37 2022 -0400
@@ -0,0 +1,104 @@
+# NextFlow DSL2 Module
+
+```bash
+AMRFINDERPLUS_RUN
+```
+
+## Description
+
+Run `amrfinder` tool on a list of assembled contigs in FASTA format. 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 file of input type `path` (`fasta`).
+
+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, organism: 'Escherichia' ]
+```
+
+\
+ 
+
+#### `fasta`
+
+Type: `path`
+
+NextFlow input type of `path` pointing to assembled contig file in FASTA format.
+
+\
+ 
+
+#### `args`
+
+Type: Groovy String
+
+String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file.
+
+Ex:
+
+```groovy
+withName: 'AMRFINDERPLUS_RUN' {
+    ext.args = '--gpipe_org'
+}
+```
+
+### `output:`
+
+___
+
+Type: `tuple`
+
+Outputs a tuple of metadata (`meta` from `input:`) and list of `amrfinder` result files (`report`).
+
+\
+ 
+
+#### `report`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `amrfinder` results table file (`.tsv`) per sample (`id:`).
+
+\
+ 
+
+#### `mutional_report`
+
+Type: `path`
+\
+Optional: `true`
+
+NextFlow output type of `path` pointing to the `amrfinder` mutation results table file (`.tsv`) per sample (`id:`). Obtaining this output will depend on the presence of the `organism` key in the metadata (`meta`). See example above.
+
+\
+ 
+
+#### `versions`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.