name: shigeifinder
description: Shigella and EIEC serotyping from assemblies
icon: false
tags:
  - shigella
  - eiec
  - fasta
  - serotype
modules:
  - shigeifinder
input:
  - meta:
    type: map
    description: |
      Groovy Map containing sample information
      e.g. [ id:'test', single_end:false ]
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 shigeifinder result
      pattern: "*.tsv"
  - merged_tsv:
      type: file
      description: A merged TSV of all shigeifinder result files
      pattern: "shigeifinder.tsv"
  - versions:
      type: file
      description: File containing software versions
      pattern: 'versions.yml'
docs:
  meta:
    title: shigeifinder
    description: >-
      A Bactopia Tool which uses ShigEiFinder to conduct _in silico_ prediction
      of serotype for Shigella and EIEC genomes.
  introduction: |
    The `shigeifinder` module used [ShigEiFinder](https://github.com/LanLab/ShigEiFinder) to conduct
    _in silico_ prediction of serotype for Shigella and EIED. It uses the genome assemblies
    tp provide basic species identification and the predicted serotype (e.g. O174:H21).
  output:
    tree: |
      <BACTOPIA_DIR>
      ├── <SAMPLE_NAME>
      │   └── tools
      │       └── shigeifinder
      │           ├── GCF_016726285.tsv
      │           └── logs
      │               ├── nf-shigeifinder.{begin,err,log,out,run,sh,trace}
      │               └── versions.yml
      └── bactopia-runs
          └── shigeifinder-<TIMESTAMP>
              ├── merged-results
              │   ├── logs
              │   │   └── shigeifinder-concat
              │   │       ├── nf-merged-results.{begin,err,log,out,run,sh,trace}
              │   │       └── versions.yml
              │   └── shigeifinder.tsv
              └── nf-reports
                  ├── shigeifinder-dag.dot
                  ├── shigeifinder-report.html
                  ├── shigeifinder-timeline.html
                  └── shigeifinder-trace.txt
    add_note: true
    folders:
      - name: Merged Results
        description: |
          Below are results that are concatenated into a single file.
        table:
          - id: shigeifinder.tsv
            description: A merged TSV file with `ShigEiFinder` results from all samples
      - name: ShigEiFinder
        description: |
          Below is a description of the _per-sample_ results from [ShigEiFinder](https://github.com/LanLab/ShigEiFinder).
        is_extensions: true
        table:
          - id: <SAMPLE_NAME>.tsv
            description: A tab-delimited file with the predicted Shigella or EIEC serotype
  citations:
    - csvtk
    - shigeifinder
