From 0ea3fa6690518a3556c880e1da8ab6fcd27c5ca6 Mon Sep 17 00:00:00 2001 From: Thomas Battenfeld Date: Sun, 19 Dec 2021 19:00:55 +0100 Subject: [PATCH] add docs --- docs/user-guide/configuration.md | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/docs/user-guide/configuration.md b/docs/user-guide/configuration.md index a025a48b1..8edc7d9f7 100644 --- a/docs/user-guide/configuration.md +++ b/docs/user-guide/configuration.md @@ -1 +1,16 @@ # Configuration + +## Execution Mode + +Accepted values: `patient`, `environment`. Defaults to `patient`. + +Defines the execution mode of UnCoVar. + +When the mode is set to `patient`, the sample is assumed to be from a single +host organism and contains only one strain of SARS-CoV-2. The parts of the +workflow responsible for reconstructing this SARS-CoV-2 strain genome are activated. + +If the mode is set to `environment`, the sample is assumed to be from the +environment (e.g. wastewater) and to contain different SARS-CoV-2 strains. +The parts of the workflow responsible for creating and analysing individual +genomes (e.g. assembly, lineage calling via Pangolin) are disabled.