GArcho44/snvs-annotation-pipeline

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Overview

Latest release: None, Last update: 2025-12-12

Linting: linting: failed, Formatting: formatting: failed

Deployment

Step 1: Install Snakemake and Snakedeploy

Snakemake and Snakedeploy are best installed via the Conda. It is recommended to install conda via Miniforge. Run

conda create -c conda-forge -c bioconda -c nodefaults --name snakemake snakemake snakedeploy

to install both Snakemake and Snakedeploy in an isolated environment. For all following commands ensure that this environment is activated via

conda activate snakemake

For other installation methods, refer to the Snakemake and Snakedeploy documentation.

Step 2: Deploy workflow

With Snakemake and Snakedeploy installed, the workflow can be deployed as follows. First, create an appropriate project working directory on your system and enter it:

mkdir -p path/to/project-workdir
cd path/to/project-workdir

In all following steps, we will assume that you are inside of that directory. Then run

snakedeploy deploy-workflow https://github.com/GArcho44/snvs-annotation-pipeline . --tag None

Snakedeploy will create two folders, workflow and config. The former contains the deployment of the chosen workflow as a Snakemake module, the latter contains configuration files which will be modified in the next step in order to configure the workflow to your needs.

Step 3: Configure workflow

To configure the workflow, adapt config/config.yml to your needs following the instructions below.

Step 4: Run workflow

The deployment method is controlled using the --software-deployment-method (short --sdm) argument.

To run the workflow using apptainer/singularity, use

snakemake --cores all --sdm apptainer

To run the workflow using a combination of conda and apptainer/singularity for software deployment, use

snakemake --cores all --sdm conda apptainer

To run the workflow with automatic deployment of all required software via conda/mamba, use

snakemake --cores all --sdm conda

Snakemake will automatically detect the main Snakefile in the workflow subfolder and execute the workflow module that has been defined by the deployment in step 2.

For further options such as cluster and cloud execution, see the docs.

Step 5: Generate report

After finalizing your data analysis, you can automatically generate an interactive visual HTML report for inspection of results together with parameters and code inside of the browser using

snakemake --report report.zip

Configuration

The following section is imported from the workflow’s config/README.md.

Workflow overview

This workflow is a best-practice workflow for <structure-aware annotation of microbial SNPs>. The workflow is built using snakemake and consists of the following 3 main configurable modules:

  • A. Sequence-based functional annotation of SNPs & Genes (later release)

  • B. Retrieval of high-confidence structure models from AFDB and ESMatlas protein structure databases

  • C. Measurement and prediction of structure-aware properties for protein residues affected from missense SNPs

Running the workflow

Input data

  1. Species-specific identifier

  2. A variant calling file (.vcf) that follows the required format (see example)

  3. A gene annotation file (.gff or .tsv) that follows the required format (see example)

  4. All protein sequences for the annotated genes in a single fasta file (.fasta)

  5. Diamond database (.dmnd) of protein sequences in AlphaFold Database

  6. Diamond database (.dmnd) of protein sequences in ESMatlas Database

*Note: later releases will provide more generalized input files

Parameters

This table lists all parameters that can be adjusted/modified to run the workflow.

parameter

type

details

default

species

species_id

str

species-specific identifier

snps_annotation

path

str

path to snps annotation file

genes_annotation

path

str

path to genes annotation file

protein_db

path

str

path to protein sequences .fasta file

afdb_diamond_db

path

str

path to AlphaFold Diamond database file (.dmnd)

esm_diamond_db

path

str

path to ESMatlas Diamond database file (.dmnd)

Execute the workflow

snakemake –software-deployment-method conda –cores 1 all –config species=101157

Linting and formatting

Linting results

1WorkflowError in file "/tmp/tmpi_s7seo7/workflow/Snakefile", line 5:
2Workflow defines configfile ../config/config.yml but it is not present or accessible (full checked path: /tmp/config/config.yml).

Formatting results

1[DEBUG] 
2[DEBUG] In file "/tmp/tmpi_s7seo7/workflow/Snakefile":  Formatted content is different from original
3[INFO] 1 file(s) would be changed 😬
4
5snakefmt version: 0.11.2