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.
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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