kkonganti@0: # NextFlow DSL2 Module
kkonganti@0: 
kkonganti@0: ```bash
kkonganti@0: SEQSERO2
kkonganti@0: ```
kkonganti@0: 
kkonganti@0: ## Description
kkonganti@0: 
kkonganti@0: Run `seqsero2` tool on a list of assembled *Salmonella* contigs in FASTA format or sequencing reads in FASTQ format.
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: ### `input:`
kkonganti@0: 
kkonganti@0: ___
kkonganti@0: 
kkonganti@0: Type: `tuple`
kkonganti@0: 
kkonganti@0: Takes in the following tuple of metadata (`meta`) and a list of assemled contig FASTA files or list of sequencing reads in FASTQ format of input type `path` (`reads_or_asm`).
kkonganti@0: 
kkonganti@0: Ex:
kkonganti@0: 
kkonganti@0: ```groovy
kkonganti@0: [ [id: 'sample1', single_end: true], '/data/sample1/f_assembly.fa' ]
kkonganti@0: ```
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `meta`
kkonganti@0: 
kkonganti@0: Type: Groovy Map
kkonganti@0: 
kkonganti@0: A Groovy Map containing the metadata about the FASTQ files or assembly FASTA files.
kkonganti@0: 
kkonganti@0: Ex:
kkonganti@0: 
kkonganti@0: ```groovy
kkonganti@0: [ id: 'FAL00870', strandedness: 'unstranded', single_end: true ]
kkonganti@0: ```
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `reads_or_asm`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: 
kkonganti@0: NextFlow input type of `path` pointing to assembled contig file in FASTA format or sequencing reads in FASTQ format.
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `args`
kkonganti@0: 
kkonganti@0: Type: Groovy String
kkonganti@0: 
kkonganti@0: 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@0: 
kkonganti@0: Ex:
kkonganti@0: 
kkonganti@0: ```groovy
kkonganti@0: withName: 'SEQSERO2' {
kkonganti@0:     ext.args = '-b mem'
kkonganti@0: }
kkonganti@0: ```
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: ### `output:`
kkonganti@0: 
kkonganti@0: ___
kkonganti@0: 
kkonganti@0: Type: `tuple`
kkonganti@0: 
kkonganti@0: Outputs a tuple of metadata (`meta` from `input:`) and list of `seqsero2` result files (`serotyped`).
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `serotyped`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: 
kkonganti@0: NextFlow output type of `path` pointing to the `seqsero2` results table file per sample (`id:`).
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `versions`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: 
kkonganti@0: NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.