MiGA Manual
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Introduction
Part I: What is MiGA?
Part II: Getting started
Part III: Interfaces
Part IV: Deploying examples
Part V: Additional details
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. 1.
    ​Quality​
  2. 2.
    ​Dereplicate​
  3. 3.
    ​Classify​
  4. 4.
    ​Preprocess​
  5. 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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