TMs-code/phagefactor

Structure-aware functional annotation of phage genomes.

Overview

Latest release: v1.2.0, Last update: 2026-10-29

Share link: https://snakemake.github.io/snakemake-workflow-catalog?wf=TMs-code/phagefactor

Quality control: linting: failed formatting: failed

Topics: curation-tool phage-genomics structure-prediction

Workflow Rule Graph

This visualization of the workflow’s rule graph was automatically generated using Snakevision

Deployment

Step 1: Install Snakemake and Snakedeploy

Snakemake and Snakedeploy are best installed via the Conda package manager. 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/TMs-code/phagefactor . --tag v1.2.0

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 4: Run workflow

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

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.

Configuration

phageFACTor reads two files from the config/ folder of the directory it is launched from (the project dir):

File	Holds	Edit before the first run
`config.yaml`	the science: database locations, FoldSeek tiers, curation thresholds, host genus	`databases.db_root`, `project.host_genus`
`workflow.yaml`	what to run and where: input/search mode, Phynteny on/off, SLURM partition/QOS, resources per step	optional (every key defaults to a sensible value)

Full reference: docs/configure.md.

Input

Put the sequences in input/fasta/ next to config/:

genome mode: one nucleotide FASTA per prophage, plus input/prophage_list.txt with one prophage name (FASTA file stem) per line;
protein mode: one or more protein FASTA files (.faa);
pangenome mode: one nucleotide FASTA of gene sequences.

The mode is detected from the FASTA files (input_mode: auto). Details: docs/modes.md.

Databases

The databases (Pharokka, Phold, FoldSeek: AFDB-SwissProt, PDB100, optionally AFDB50) are not downloaded by the workflow. Download them once per machine and set databases.db_root in config/config.yaml to their folder:

conda create -n phagefactor -c conda-forge -c bioconda phagefactor   # provides the helper
conda run -n phagefactor phagefactor databases /path/to/db_dir --all

docs/databases.md lists the sizes and how to download only a subset (the FoldSeek search can also run on the FoldSeek web server: search_mode: webapi).

Running as a Snakemake module

Deployed with snakedeploy, the workflow runs with plain Snakemake:

snakedeploy deploy-workflow https://github.com/TMs-code/phagefactor . --tag v1.2.0
snakemake --cores all --sdm conda                     # this machine
snakemake --sdm conda --executor slurm --jobs 50      # SLURM

The config handed to the module may hold both files’ keys: the sections of config.yaml (project, paths, databases, foldseek, compare, curate, phynteny, precomputed) are merged over config/config.yaml, every other key is a workflow.yaml setting. --config phynteny=false switches Phynteny off.

With --sdm conda, Snakemake builds envs/phagefactor.yaml and envs/phynteny.yaml itself; the first Phynteny job downloads its models into the env (needs internet). The Phold database must then be in <db_root>/phold_db (or databases.phold_db): a Phold database installed inside another env is not seen. Without --sdm conda, jobs run in the named environments set by tools_env / phynteny_env (see docs/snakemake.md).

Linting and formatting

Linting results

/home/runner/work/snakemake-workflow-catalog/snakemake-workflow-catalog/.pixi/envs/default/lib/python3.13/site-packages/google/auth/transport/grpc.py:43: FutureWarning: grpcio < 1.83.0 does not support Post-Quantum Cryptography (PQC). Support for non-PQC environments is deprecated. In April 2027, google-auth will raise its minimum requirements to enforce grpcio >= 1.83.0. For more details on Google Cloud's post-quantum security migration, visit: https://cloud.google.com/security/resources/post-quantum-cryptography
  warnings.warn(
Creating specified working directory /tmp/tmpz1hsuvb8/TMs-code-phagefactor-90c3d42/runs/run.
WorkflowError in file "/tmp/tmpz1hsuvb8/TMs-code-phagefactor-90c3d42/workflow/Snakefile", line 290:
Input auto-detection failed:
ERROR: FASTA directory not found: /tmp/tmpz1hsuvb8/TMs-code-phagefactor-90c3d42/input/fasta
Set it explicitly: --config input_mode=genome|protein|pangenome
  File "/tmp/tmpz1hsuvb8/TMs-code-phagefactor-90c3d42/workflow/Snakefile", line 290, in <module>

Formatting results

[DEBUG] 
[DEBUG] In file "/tmp/tmpz1hsuvb8/TMs-code-phagefactor-90c3d42/workflow/Snakefile":  Formatted content is different from original
[INFO] 1 file(s) would be changed 😬

snakefmt version: 0.11.5