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Concepts
========

PSOT is a system that executes bioinformatic tools on a file with protein
sequences and converts the results into easy to process json documents. It
contains a live mode that writes the results of already finished tools into
a directory, which can be polled and further processed, e.g. by a website
that displays results as they become ready.

Vocabulary
----------

Module
    A module implements a bioinformatic tool and the corresponding json converter.
    It is defined in a module manifest.

Profile
    A profile is a set of modules that are executed during an execution of PSOT.
    Profiles can override default parameters of modules.

Workflow
--------

1. Load all module manifests and profiles
2. Create an execution directory
3. Generate a nextflow script for the choosen profile in the execution directory
4. Run the nextflow script
5. Remove the execution directory

Structure of the Nextflow Script
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1. Run all analyses in parallel
2. Convert all analyses in parallel
3. In live mode: generate a json document for each module and each sequence within the live directory
4. Join all json files into a single one containing all information
5. Split the large json file into separate files for each sequence