name: ssuissero
description: Serotype prediction of _Streptococcus suis_ assemblies
keywords:
  - bacteria
  - fasta
  - streptococcus
modules:
  - ssuissero
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: The final assembly in FASTA format
      pattern: "*.{fna,fna.gz}"
output:
  - tsv:
      type: file
      description: A summary of the per-sample serotype predictions
      pattern: "*.tsv"
  - merged_tsv:
      type: file
      description: A merged TSV of all serotype predictions
      pattern: "ectyper.tsv"
  - versions:
      type: file
      description: File containing software versions
      pattern: 'versions.yml'
docs:
  meta:
    title: ssuissero
    description: >-
      A Bactopia Tool which uses SsuisSero to predict the serotype of
      _Streptococcus suis_ assemblies.
  introduction: |
    The `ssuissero` module uses [SsuisSero](https://github.com/jimmyliu1326/SsuisSero) to predict
    the serotype of _Streptococcus suis_ assemblies.
  output:
    tree: |
      <BACTOPIA_DIR>
      ├── <SAMPLE_NAME>
      │   └── tools
      │       └── ssuissero
      │           ├── <SAMPLE_NAME>_serotyping_res.tsv
      │           └── logs
      │               ├── nf-ssuissero.{begin,err,log,out,run,sh,trace}
      │               └── versions.yml
      └── bactopia-runs
          └── ssuissero-<TIMESTAMP>
              ├── merged-results
              │   ├── logs
              │   │   └── ssuissero-concat
              │   │       ├── nf-merged-results.{begin,err,log,out,run,sh,trace}
              │   │       └── versions.yml
              │   └── ssuissero.tsv
              └── nf-reports
                  ├── ssuissero-dag.dot
                  ├── ssuissero-report.html
                  ├── ssuissero-timeline.html
                  └── ssuissero-trace.txt
    add_note: true
    folders:
      - name: Merged Results
        description: |
          Below are results that are concatenated into a single file.
        table: 
          - id: ssuissero.tsv
            description: A merged TSV file with `SsuisSero` results from all samples
      - name: SsuisSero
        description: |
          Below is a description of the _per-sample_ results from [SsuisSero](https://github.com/jimmyliu1326/SsuisSero).
        table:
          - id: <SAMPLE_NAME>_serotyping_res.tsv
            description: A tab-delimited file with `SsuisSero` results
  citations:
    - csvtk
    - ssuissero
