name: quast
description: A module for assessing the quality of assembled contigs
icon: false
keywords:
  - assembly
  - quality
modules:
  - quast
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"
docs:
  meta:
    title: quast
    description: >
      A Bactopia Tool which uses QUAST to assess the quality of assembled contigs.
  introduction: |
      The `quast` module uses [QUAST](https://github.com/ablab/quast) to assess the quality of
      assembled contigs. To assist assessment, QUAST produces a number of plots and tables that
      can be evaluated.
  output:
    tree: |
      <BACTOPIA_DIR>
      ├── <SAMPLE_NAME>
      │   └── tools
      │       └── quast
      │           ├── <SAMPLE_NAME>.tsv
      │           ├── basic_stats/
      │           ├── icarus.html
      │           ├── icarus_viewers
      │           │   └── contig_size_viewer.html
      │           ├── logs
      │           │   ├── nf-quast.{begin,err,log,out,run,sh,trace}
      │           │   ├── quast.log
      │           │   └── versions.yml
      │           ├── predicted_genes
      │           │   ├── <SAMPLE_NAME>.stderr
      │           │   └── <SAMPLE_NAME>_glimmer_genes.gff
      │           ├── report.{html|pdf|tex|tsv|txt}
      │           └── transposed_report.{tex|tsv|txt}
      └── bactopia-runs
          └── quast-<TIMESTAMP>
              ├── merged-results
              │   ├── logs
              │   │   └── quast-concat
              │   │       ├── nf-merged-results.{begin,err,log,out,run,sh,trace}
              │   │       └── versions.yml
              │   └── quast.tsv
              └── nf-reports
                  ├── quast-dag.dot
                  ├── quast-report.html
                  ├── quast-timeline.html
                  └── quast-trace.txt
    add_note: false
    folders:
      - name: Merged Results
        description: |
          Below are results that are concatenated into a single file.
        table:
          - id: <SAMPLE_NAME>.tsv
            description: A summary of the quast results for all samples
      - name: QUAST
        description: |
          Below is a description of the _per-sample_ results from [QUAST](https://github.com/ablab/quast).
        table:
          - id: basic_stats/
            description: A folder with plots of assembly metrics (e.g. GC content, NGx, Nx)
          - id: icarus.html
            description: Icarus main menu with links to interactive viewers.
          - id: icarus_viewers/
            description: Additional reports for Icarus
          - id: predicted_genes/
            description: Predicted gene output
          - id: quast.log
            description: Detailed information about the QUAST run
          - id: 'report.{html\|pdf\|tex\|tsv\|txt}'
            description: Assessment summary including all tables and plots
          - id: 'transposed_report.{tex\|tsv\|txt}'
            description: Transposed version of the assessment summary
  citations:
    - csvtk
    - quast
