richardstoeckl/prokanota

prokanota - Flexible pipeline for prokaryotic annotation

Overview

Topics:

Latest release: 1.1.0, Last update: 2025-03-24

Linting: linting: failed, Formatting: formatting: failed

Deployment

Step 1: Install Snakemake and Snakedeploy

Snakemake and Snakedeploy are best installed via the Mamba package manager (a drop-in replacement for conda). If you have neither Conda nor Mamba, it is recommended to install Miniforge. More details regarding Mamba can be found here.

When using Mamba, run

mamba create -c conda-forge -c bioconda --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

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/richardstoeckl/prokanota . --tag 1.1.0

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 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 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.

General configuration

To configure this workflow, modify config/config.yaml and config/metadata.csv according to your needs, following the explanations provided in the file.

Pipeline configuration

To successfully run the annotation pipeline, you will need to configure the paths to the databases and the output directories in the config/config.yaml file.

Sample setup

The sample setup is specified via comma-separated tabular file (.csv). Missing values can be specified by empty columns.

Sample sheet

The default sample sheet is config/metadata.csv (as configured in config/config.yaml). Each row usually corresponds to one genome with the first collumn being the sampleID (Note: The sampleID is used to name the output files and is used to calculate the gene_ids!), and the second column being the path to the genome assembly in FASTA format.

Linting and formatting

Linting results

1WorkflowError in file /tmp/tmpgdt8am4b/richardstoeckl-prokanota-a6b001a/workflow/Snakefile, line 19:
2Expecting Snakemake version 8.27.1 or higher (you are currently using 8.25.5).

Formatting results

 1[DEBUG] 
 2[DEBUG] In file "/tmp/tmpgdt8am4b/richardstoeckl-prokanota-a6b001a/workflow/Snakefile":  Formatted content is different from original
 3[DEBUG] 
 4[DEBUG] In file "/tmp/tmpgdt8am4b/richardstoeckl-prokanota-a6b001a/workflow/rules/prepProteins.smk":  Formatted content is different from original
 5[DEBUG] 
 6[WARNING] In file "/tmp/tmpgdt8am4b/richardstoeckl-prokanota-a6b001a/workflow/rules/prepDBs.smk":  Keyword "output" at line 156 has comments under a value.
 7	PEP8 recommends block comments appear before what they describe
 8(see https://www.python.org/dev/peps/pep-0008/#id30)
 9[DEBUG] In file "/tmp/tmpgdt8am4b/richardstoeckl-prokanota-a6b001a/workflow/rules/prepDBs.smk":  Formatted content is different from original
10[DEBUG] 
11[DEBUG] In file "/tmp/tmpgdt8am4b/richardstoeckl-prokanota-a6b001a/workflow/rules/searchDBs.smk":  Formatted content is different from original
12[DEBUG] 
13[DEBUG] In file "/tmp/tmpgdt8am4b/richardstoeckl-prokanota-a6b001a/workflow/rules/parseSearchResults.smk":  Formatted content is different from original
14[INFO] 5 file(s) would be changed 😬
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16snakefmt version: 0.10.2