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+++ b/0.7.0/modules/abricate/summary/README.md	Mon Jul 15 10:42:02 2024 -0400
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+# NextFlow DSL2 Module
+
+```bash
+ABRICATE_SUMMARY
+```
+
+## Description
+
+Run `abricate` tool's `summary` sub-command on a list of `abricate`'s result table files per database.
+
+\
+ 
+
+### `input:`
+
+___
+
+Type: `tuple`
+
+Takes in the following tuple of `abricate` database names of type `val` (`abdbs`) and a list of `abricate` result table files for all databases of type `path` (`abfiles`).
+
+Ex:
+
+```groovy
+[ 
+    [ 'megares', 'argannot', 'resfinder', 'ncbi' ], 
+    [ '/data/sample1/f.ncbi.ab.txt',
+      '/data/sample1/f.megares.ab.txt',
+      '/data/sample1/f.resfinder.ab.txt',
+      '/data/sample1/f.argannot.ab.txt',
+      '/data/sample1/f2.ncbi.ab.txt',
+      '/data/sample1/f2.megares.ab.txt',
+      '/data/sample1/f2.resfinder.ab.txt',
+      '/data/sample1/f2.argannot.ab.txt'
+    ]
+]
+```
+
+\
+ 
+
+#### `abdbs`
+
+Type: `val`
+
+A Groovy List containing the **mandatory** list of at least the following 4 `abricate` database names on which `abricate` was run.
+
+Ex:
+
+```groovy
+[ 'resfinder', 'megares', 'ncbi', 'argannot' ]
+```
+
+\
+ 
+
+#### `abfiles`
+
+Type: `path`
+
+NextFlow input type of `path` pointing to `abricate` result files for each of the database.
+
+\
+ 
+
+### `output:`
+
+___
+
+#### `ncbi`
+
+Type: `tuple`
+\
+Optional: `true`
+
+Outputs a tuple of `abricate` database key (`abricate_ncbi`) and summary result file from `abricate summary` command of type `path` (`ncbi`). This database includes only core AMR genes. This tuple is emitted optionally only where there are output files with suffix `.ncbi.absum.txt`
+
+\
+ 
+
+#### `ncbiamrplus`
+
+Type: `tuple`
+\
+Optional: `true`
+
+Outputs a tuple of `abricate` database key (`abricate_ncbiamrplus`) and summary result file from `abricate summary` command of type `path` (`ncbiamrplus`). This database includes both core AMR genes and plus AMR genes. This tuple is emitted optionally only where there are output files with suffix `.ncbiamrplus.absum.txt`
+
+\
+ 
+
+#### `resfinder`
+
+Type: `tuple`
+\
+Optional: `true`
+
+Outputs a tuple of `abricate` database key (`abricate_resfinder`) and summary result file from `abricate summary` command of type `path` (`resfinder`). This tuple is emitted optionally only where there are output files with suffix `.resfinder.absum.txt`
+
+\
+ 
+
+#### `megares`
+
+Type: `tuple`
+\
+Optional: `true`
+
+Outputs a tuple of `abricate` database key (`abricate_megares`) and summary result file from `abricate summary` command of type `path` (`megares`). This tuple is emitted optionally only where there are output files with suffix `.megares.absum.txt`
+
+\
+ 
+
+#### `argannot`
+
+Type: `tuple`
+\
+Optional: `true`
+
+Outputs a tuple of `abricate` database key (`abricate_argannot`) and summary result file from `abricate summary` command of type `path` (`argannot`). This tuple is emitted optionally only where there are output files with suffix `.argannot.absum.txt`
+
+\
+ 
+
+#### `ecoli_vf`
+
+Type: `tuple`
+\
+Optional: `true`
+
+Outputs an **optional** tuple of `abricate` database key (`abricate_ecoli_vf`) and summary result file from `abricate summary` command of type `path` (`ecoli_vf`). This tuple is emitted only when there are output files with suffix `.ecoli_vf.absum.txt` within the `work` folder.
+
+\
+ 
+
+#### `versions`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.