# NextFlow DSL2 Module

```bash
SEQSERO2
```

## Description

Run `seqsero2` tool on a list of assembled *Salmonella* contigs in FASTA format or sequencing reads in FASTQ format.

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### `input:`

___

Type: `tuple`

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`).

Ex:

```groovy
[ [id: 'sample1', single_end: true], '/data/sample1/f_assembly.fa' ]
```

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#### `meta`

Type: Groovy Map

A Groovy Map containing the metadata about the FASTQ files or assembly FASTA files.

Ex:

```groovy
[ id: 'FAL00870', strandedness: 'unstranded', single_end: true ]
```

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#### `reads_or_asm`

Type: `path`

NextFlow input type of `path` pointing to assembled contig file in FASTA format or sequencing reads in FASTQ format.

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#### `args`

Type: Groovy String

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.

Ex:

```groovy
withName: 'SEQSERO2' {
    ext.args = '-b mem'
}
```

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### `output:`

___

Type: `tuple`

Outputs a tuple of metadata (`meta` from `input:`) and list of `seqsero2` result files (`serotyped`).

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#### `serotyped`

Type: `path`

NextFlow output type of `path` pointing to the `seqsero2` results table file per sample (`id:`).

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#### `versions`

Type: `path`

NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.