Pipeline Overview¶

An overview of the sequencing pipelines is shown below.

Note

The full protocol (in development) can be found here

The main pipeline for a project involves quality control, trimming, mapping, and variant calling using GATK4.

Parameters:
- config_main.yaml: YAML configuration file containing project details and workflow parameters.

Functions:
- spend_time(start_time, end_time): Calculates the time spent between two given time points and returns it in the format "hours:minutes:seconds".

Workflow Steps:
1. Read the configuration file. 2. Check if quality control is required. - If yes, perform quality control using Snakemake and log the running time. - If no, check if trimming is required. - If yes, perform trimming using Snakemake and log the running time. - If no, skip trimming step. 3. Perform mapping using Snakemake and log the running time. 4. Perform variant calling using GATK4 using Snakemake and log the running time.