name: mcroni
description: Sequence variation in mcr-1 genes (mobilized colistin resistance)
icon: false
keywords:
  - fasta
  - antimicrobial resistance
modules:
  - mcroni
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 ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - merged_tsv:
      type: file
      description: A merged TSV of mcroni results from all samples
      pattern: "*.tsv"
  - tsv:
      type: file
      description: per-sample mcroni results in TSV format
      pattern: "*.tsv"
  - fa:
      type: file
      description: mcr-1 matching sequences
      pattern: "*.fa"
docs:
  meta:
    title: mcroni
    description: >-
      A Bactopia Tool which uses mcroni to identify _mcr-1_ genes in 
      assemblies.
  introduction: |
      The `mcroni` module uses [mcroni](https://github.com/liampshaw/mcroni) to identify _mcr-1_ genes in 
      assemblies. If _mcr-1_ is found, the variations will be reported and available in an output FASTA file.
  output:
    tree: |
      <BACTOPIA_DIR>
      ├── <SAMPLE_NAME>
      │   └── tools
      │       └── mcroni
      │           ├── <SAMPLE_NAME>_sequence.fa
      │           ├── <SAMPLE_NAME>_table.tsv
      │           └── logs
      │               ├── nf-mcroni.{begin,err,log,out,run,sh,trace}
      │               └── versions.yml
      └── bactopia-runs
          └── mcroni-<TIMESTAMP>
              ├── merged-results
              │   ├── logs
              │   │   └── mcroni-concat
              │   │       ├── nf-merged-results.{begin,err,log,out,run,sh,trace}
              │   │       └── versions.yml
              │   └── mcroni.tsv
              └── nf-reports
                  ├── mcroni-dag.dot
                  ├── mcroni-report.html
                  ├── mcroni-timeline.html
                  └── mcroni-trace.txt
    add_note: false
    folders:
      - name: Merged Results
        description: |
          Below are results that are concatenated into a single file.
        table:
          - id: mcroni.tsv
            description: A merged TSV of mcroni results from all samples
      - name: mcroni
        description: |
          Below is a description of the _per-sample_ results from [mcroni](https://github.com/liampshaw/mcroni).
        is_extensions: true
        table:
          - id: _table.tsv
            description: mcroni results in tab-delimited format
          - id: _sequence.fa
            description: Sequences matching the _mcr-1_ gene
  citations:
    - csvtk
    - mcroni
