name: lissero
description: Serogroup typing prediction for _Listeria monocytogenes_
icon: false
tags:
  - fasta
  - Listeria monocytogenes
  - serotype
modules:
  - lissero
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: A Listeria monocytogenes fasta file.
      pattern: "*.{fna,fna.gz}"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - tsv:
      type: file
      description: A summary of the per-sample lissero result
      pattern: "*.tsv"
  - merged_tsv:
      type: file
      description: A merged TSV of all lissero result files
      pattern: "lissero.tsv"
  - versions:
      type: file
      description: File containing software versions
      pattern: 'versions.yml'
docs:
  meta:
    title: lissero
    description: >-
      A Bactopia Tool which uses LisSero for _in silico_ serotype prediction
      for _Listeria monocytogenes_ assemblies.
  introduction: |
    The `lissero` module uses [LisSero](https://github.com/MDU-PHL/LisSero) for 
    _in silico_ serotype prediction for _Listeria monocytogenes_ assemblies.
  output:
    tree: |
      <BACTOPIA_DIR>
      ├── <SAMPLE_NAME>
      │   └── tools
      │       └── lissero
      │           ├── <SAMPLE_NAME>.tsv
      │           └── logs
      │               ├── nf-lissero.{begin,err,log,out,run,sh,trace}
      │               └── versions.yml
      └── bactopia-runs
          └── lissero-<TIMESTAMP>
              ├── merged-results
              │   ├── lissero.tsv
              │   └── logs
              │       └── lissero-concat
              │           ├── nf-merged-results.{begin,err,log,out,run,sh,trace}
              │           └── versions.yml
              └── nf-reports
                  ├── lissero-dag.dot
                  ├── lissero-report.html
                  ├── lissero-timeline.html
                  └── lissero-trace.txt
    add_note: true
    folders:
      - name: Merged Results
        description: |
          Below are results that are concatenated into a single file.
        table:
          - id: lissero.tsv
            description: A tab-delimited file with `LisSero` results from all samples
      - name: LisSero
        description: |
          Below is a description of the _per-sample_ results from [LisSero](https://github.com/MDU-PHL/LisSero).
        table:
          - id: <SAMPLE_NAME>.tsv
            description: A tab-delimited file with `LisSero` results
  citations:
    - csvtk
    - lissero
