MiGA Manual
AboutCodebaseMiGA Online
Primary version
Primary version
  • Introduction
  • Part I: What is MiGA?
    • How can MiGA help me?
    • Who is using MiGA?
    • Who is behind MiGA?
    • Definitions
  • Part II: Getting started
    • Requirements
      • Using Homebrew
      • Using apt-get
      • Using Conda
      • Installing from source
      • MyTaxa Utils
    • Installation
    • MiGA types
    • Input data
    • Distances
    • Clustering
  • Part III: Interfaces
    • MiGA API
    • MiGA CLI
    • MiGA Web
  • Part IV: Deploying examples
    • RefSeq in MiGA
    • Build a clade collection
    • Launching daemons
    • Setting up MiGA in a cluster
  • Part V: Additional details
    • Advanced configuration
    • MiGA workflow
    • Metadata
    • External Software
  • Part VI: Workflows
    • Quality
    • Dereplicate
    • Classify
    • Preprocess
    • Index
    • Summaries
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Part VI: Workflows

CLI Workflows automate common tasks in MiGA. Currently implemented workflows include:

  1. Quality

  2. Dereplicate

  3. Classify

  4. Preprocess

  5. Index

Using multiple workflows

It is possible to concatenate workflows in the same project. First, run the first workflow as described in the documentation. For example:

miga quality_wf -o my_project /path/to/genomes/*.fna

Next, execute any additional steps without specifying the input files, and using the same output directory. For example:

miga classify_wf -o my_project
miga rerep_wf -o my_project

In the examples above, input genomes will be processed to evaluate quality, next they'll be classified, and finally they'll be dereplicated.

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Last updated 5 years ago