kkonganti@105: # NextFlow DSL2 Module
kkonganti@105: 
kkonganti@105: ```bash
kkonganti@105: AMRFINDERPLUS_RUN
kkonganti@105: ```
kkonganti@105: 
kkonganti@105: ## Description
kkonganti@105: 
kkonganti@105: Run `amrfinder` tool on a list of assembled contigs in FASTA format. Produces a single output table in ASCII text format per database.
kkonganti@105: 
kkonganti@105: \
kkonganti@105:  
kkonganti@105: 
kkonganti@105: ### `input:`
kkonganti@105: 
kkonganti@105: ___
kkonganti@105: 
kkonganti@105: Type: `tuple`
kkonganti@105: 
kkonganti@105: Takes in the following tuple of metadata (`meta`) and a list of assemled contig FASTA file of input type `path` (`fasta`).
kkonganti@105: 
kkonganti@105: Ex:
kkonganti@105: 
kkonganti@105: ```groovy
kkonganti@105: [ [id: 'sample1', single_end: true], '/data/sample1/f_assembly.fa' ]
kkonganti@105: ```
kkonganti@105: 
kkonganti@105: \
kkonganti@105:  
kkonganti@105: 
kkonganti@105: #### `meta`
kkonganti@105: 
kkonganti@105: Type: Groovy Map
kkonganti@105: 
kkonganti@105: A Groovy Map containing the metadata about the FASTQ file.
kkonganti@105: 
kkonganti@105: Ex:
kkonganti@105: 
kkonganti@105: ```groovy
kkonganti@105: [ id: 'FAL00870', strandedness: 'unstranded', single_end: true, organism: 'Escherichia' ]
kkonganti@105: ```
kkonganti@105: 
kkonganti@105: \
kkonganti@105:  
kkonganti@105: 
kkonganti@105: #### `fasta`
kkonganti@105: 
kkonganti@105: Type: `path`
kkonganti@105: 
kkonganti@105: NextFlow input type of `path` pointing to assembled contig file in FASTA format.
kkonganti@105: 
kkonganti@105: \
kkonganti@105:  
kkonganti@105: 
kkonganti@105: #### `args`
kkonganti@105: 
kkonganti@105: Type: Groovy String
kkonganti@105: 
kkonganti@105: 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.
kkonganti@105: 
kkonganti@105: Ex:
kkonganti@105: 
kkonganti@105: ```groovy
kkonganti@105: withName: 'AMRFINDERPLUS_RUN' {
kkonganti@105:     ext.args = '--gpipe_org'
kkonganti@105: }
kkonganti@105: ```
kkonganti@105: 
kkonganti@105: ### `output:`
kkonganti@105: 
kkonganti@105: ___
kkonganti@105: 
kkonganti@105: Type: `tuple`
kkonganti@105: 
kkonganti@105: Outputs a tuple of metadata (`meta` from `input:`) and list of `amrfinder` result files (`report`).
kkonganti@105: 
kkonganti@105: \
kkonganti@105:  
kkonganti@105: 
kkonganti@105: #### `report`
kkonganti@105: 
kkonganti@105: Type: `path`
kkonganti@105: 
kkonganti@105: NextFlow output type of `path` pointing to the `amrfinder` results table file (`.tsv`) per sample (`id:`).
kkonganti@105: 
kkonganti@105: \
kkonganti@105:  
kkonganti@105: 
kkonganti@105: #### `mutional_report`
kkonganti@105: 
kkonganti@105: Type: `path`
kkonganti@105: \
kkonganti@105: Optional: `true`
kkonganti@105: 
kkonganti@105: 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.
kkonganti@105: 
kkonganti@105: \
kkonganti@105:  
kkonganti@105: 
kkonganti@105: #### `versions`
kkonganti@105: 
kkonganti@105: Type: `path`
kkonganti@105: 
kkonganti@105: NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.