kkonganti@101: # NextFlow DSL2 Module
kkonganti@101: 
kkonganti@101: ```bash
kkonganti@101: ABRICATE_SUMMARY
kkonganti@101: ```
kkonganti@101: 
kkonganti@101: ## Description
kkonganti@101: 
kkonganti@101: Run `abricate` tool's `summary` sub-command on a list of `abricate`'s result table files per database.
kkonganti@101: 
kkonganti@101: \
kkonganti@101:  
kkonganti@101: 
kkonganti@101: ### `input:`
kkonganti@101: 
kkonganti@101: ___
kkonganti@101: 
kkonganti@101: Type: `tuple`
kkonganti@101: 
kkonganti@101: 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`).
kkonganti@101: 
kkonganti@101: Ex:
kkonganti@101: 
kkonganti@101: ```groovy
kkonganti@101: [ 
kkonganti@101:     [ 'megares', 'argannot', 'resfinder', 'ncbi' ], 
kkonganti@101:     [ '/data/sample1/f.ncbi.ab.txt',
kkonganti@101:       '/data/sample1/f.megares.ab.txt',
kkonganti@101:       '/data/sample1/f.resfinder.ab.txt',
kkonganti@101:       '/data/sample1/f.argannot.ab.txt',
kkonganti@101:       '/data/sample1/f2.ncbi.ab.txt',
kkonganti@101:       '/data/sample1/f2.megares.ab.txt',
kkonganti@101:       '/data/sample1/f2.resfinder.ab.txt',
kkonganti@101:       '/data/sample1/f2.argannot.ab.txt'
kkonganti@101:     ]
kkonganti@101: ]
kkonganti@101: ```
kkonganti@101: 
kkonganti@101: \
kkonganti@101:  
kkonganti@101: 
kkonganti@101: #### `abdbs`
kkonganti@101: 
kkonganti@101: Type: `val`
kkonganti@101: 
kkonganti@101: A Groovy List containing the **mandatory** list of at least the following 4 `abricate` database names on which `abricate` was run.
kkonganti@101: 
kkonganti@101: Ex:
kkonganti@101: 
kkonganti@101: ```groovy
kkonganti@101: [ 'resfinder', 'megares', 'ncbi', 'argannot' ]
kkonganti@101: ```
kkonganti@101: 
kkonganti@101: \
kkonganti@101:  
kkonganti@101: 
kkonganti@101: #### `abfiles`
kkonganti@101: 
kkonganti@101: Type: `path`
kkonganti@101: 
kkonganti@101: NextFlow input type of `path` pointing to `abricate` result files for each of the database.
kkonganti@101: 
kkonganti@101: \
kkonganti@101:  
kkonganti@101: 
kkonganti@101: ### `output:`
kkonganti@101: 
kkonganti@101: ___
kkonganti@101: 
kkonganti@101: #### `ncbi`
kkonganti@101: 
kkonganti@101: Type: `tuple`
kkonganti@101: \
kkonganti@101: Optional: `true`
kkonganti@101: 
kkonganti@101: 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`
kkonganti@101: 
kkonganti@101: \
kkonganti@101:  
kkonganti@101: 
kkonganti@101: #### `ncbiamrplus`
kkonganti@101: 
kkonganti@101: Type: `tuple`
kkonganti@101: \
kkonganti@101: Optional: `true`
kkonganti@101: 
kkonganti@101: 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`
kkonganti@101: 
kkonganti@101: \
kkonganti@101:  
kkonganti@101: 
kkonganti@101: #### `resfinder`
kkonganti@101: 
kkonganti@101: Type: `tuple`
kkonganti@101: \
kkonganti@101: Optional: `true`
kkonganti@101: 
kkonganti@101: 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`
kkonganti@101: 
kkonganti@101: \
kkonganti@101:  
kkonganti@101: 
kkonganti@101: #### `megares`
kkonganti@101: 
kkonganti@101: Type: `tuple`
kkonganti@101: \
kkonganti@101: Optional: `true`
kkonganti@101: 
kkonganti@101: 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`
kkonganti@101: 
kkonganti@101: \
kkonganti@101:  
kkonganti@101: 
kkonganti@101: #### `argannot`
kkonganti@101: 
kkonganti@101: Type: `tuple`
kkonganti@101: \
kkonganti@101: Optional: `true`
kkonganti@101: 
kkonganti@101: 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`
kkonganti@101: 
kkonganti@101: \
kkonganti@101:  
kkonganti@101: 
kkonganti@101: #### `ecoli_vf`
kkonganti@101: 
kkonganti@101: Type: `tuple`
kkonganti@101: \
kkonganti@101: Optional: `true`
kkonganti@101: 
kkonganti@101: 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.
kkonganti@101: 
kkonganti@101: \
kkonganti@101:  
kkonganti@101: 
kkonganti@101: #### `versions`
kkonganti@101: 
kkonganti@101: Type: `path`
kkonganti@101: 
kkonganti@101: NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.