miptools_analysis_no_jupyter

This is a snakemake pipeline for running a modified analysis_template_with_qual notebook (from miptools analysis). It consists of three parts:

• setup_run: creates a singularity profile for running remaining steps
• check_run_stats: checks which samples and mips worked and at what levels
• variant_calling: calls variants and generates output tables

Currently each step requires that the previous steps have run - you can't check run stats without setting up the singularity profile, and you can't run the variant calling step without setting up the run and checking run stats.

Installation

• Install conda: https://github.com/conda-forge/miniforge#unix-like-platforms-mac-os--linux. You'll need to follow the instructions to 'initialize' the conda environment at the end of the installer, then sign out and back in again.
• Create a conda environment and install snakemake there:

mamba create -c conda-forge -c bioconda -n snakemake snakemake
conda activate snakemake

Setup your environment:

• Change directory to a folder where you want to run the analysis
• Download the files of this repository into that folder

Usage:

• Edit the miptools_analysis_no_jupyter.yaml file to point to your files. Use a text editor that outputs unix line endings (e.g. vscode, notepad++, gedit, micro, emacs, vim, vi, etc.)
• If snakemake is not your active conda environment, activate snakemake with:

conda activate snakemake

• To setup your singularity environment, use:

snakemake -s setup_run.smk --cores 4

• To check run stats, use:

snakemake -s check_run_stats.smk --profile singularity_profile

• To run variant calling, use:

snakemake -s variant_calling.smk --profile singularity_profile

• to run all three steps at once, use:

bash run_all_steps.sh