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

parent 5b3d5301
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.
A module implements a bioinformatic tool and the corresponding json converter.
It is defined in a module manifest.
A profile is a set of modules that are executed during an execution of PSOT.
Profiles can override default parameters of modules.
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:
.. highlight:: yaml
......@@ -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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