kkonganti@17: # NextFlow DSL2 Module
kkonganti@17: 
kkonganti@17: ```bash
kkonganti@17: MLST
kkonganti@17: ```
kkonganti@17: 
kkonganti@17: ## Description
kkonganti@17: 
kkonganti@17: Run `mlst` tool on a list of assembled contigs in FASTA format. Produces a single output table in ASCII text format.
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: ### `input:`
kkonganti@17: 
kkonganti@17: ___
kkonganti@17: 
kkonganti@17: Type: `tuple`
kkonganti@17: 
kkonganti@17: Takes in the following tuple of metadata (`meta`) and a list of assemled contig FASTA files of input type `path` (`fasta`).
kkonganti@17: 
kkonganti@17: Ex:
kkonganti@17: 
kkonganti@17: ```groovy
kkonganti@17: [ [id: 'sample1', single_end: true], '/data/sample1/f_assembly.fa' ]
kkonganti@17: ```
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: #### `meta`
kkonganti@17: 
kkonganti@17: Type: Groovy Map
kkonganti@17: 
kkonganti@17: A Groovy Map containing the metadata about the FASTQ file.
kkonganti@17: 
kkonganti@17: Ex:
kkonganti@17: 
kkonganti@17: ```groovy
kkonganti@17: [ id: 'FAL00870', strandedness: 'unstranded', single_end: true ]
kkonganti@17: ```
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: #### `fasta`
kkonganti@17: 
kkonganti@17: Type: `path`
kkonganti@17: 
kkonganti@17: NextFlow input type of `path` pointing to assembled contig file in FASTA format.
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: #### `args`
kkonganti@17: 
kkonganti@17: Type: Groovy String
kkonganti@17: 
kkonganti@17: 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@17: 
kkonganti@17: Ex:
kkonganti@17: 
kkonganti@17: ```groovy
kkonganti@17: withName: 'MLST' {
kkonganti@17:     ext.args = '--nopath'
kkonganti@17: }
kkonganti@17: ```
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: ### `output:`
kkonganti@17: 
kkonganti@17: ___
kkonganti@17: 
kkonganti@17: Type: `tuple`
kkonganti@17: 
kkonganti@17: Outputs a tuple of metadata (`meta` from `input:`) and list of `mlst` result files (`tsv`).
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: #### `tsv`
kkonganti@17: 
kkonganti@17: Type: `path`
kkonganti@17: 
kkonganti@17: NextFlow output type of `path` pointing to the `mlst` results table file per sample (`id:`).
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: #### `versions`
kkonganti@17: 
kkonganti@17: Type: `path`
kkonganti@17: 
kkonganti@17: NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.