Commit 9139aefe authored by Lukas Jelonek's avatar Lukas Jelonek
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Add chapter on concepts

parent 5b3d5301
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
----------------------------
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
......@@ -10,6 +10,7 @@ Welcome to PSOT - protein sequence observation tool's documentation!
:maxdepth: 2
:caption: Contents:
concepts
modules
......
.. highlight:: yaml
Modules
=======
......@@ -45,3 +46,4 @@ A module manifest has the following structure::
dbxref: UniProtKB/Swiss-Prot
These parameters can be overridden in the profile.
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