young5454/ABComp

ABComp : Assembly Polishing and Bacterial Whole-genome Comparison Pipeline for Multi-group Clinical Isolates

Overview

Topics:

Latest release: None, Last update: 2024-12-07

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/young5454/ABComp . --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 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 file

ABComp requires two configuration files for running the pipeline. These yaml files can be found in the config/ directory.

config.yml is a default configuration setting for the overall Snakemake run. Make sure you specify the correct parameters and directory names of your preference.

groups_original.yml is a configuration file for the complete group-strain information of your clinical isolates. Below is an example yaml file of a 2-group, 5-strain setting :

NONMDR:
    - B0112
    - C0234
    - C3455
MDR:
    - B0232
    - D0991

Linting and formatting

Linting results

Lints for snakefile /tmp/tmpf06e0zdf/workflow/Snakefile:
    * Path composition with '+' in line 82:
      This becomes quickly unreadable. Usually, it is better to endure some
      redundancy against having a more readable workflow. Hence, just repeat
      common prefixes. If path composition is unavoidable, use pathlib or
      (python >= 3.6) string formatting with f"...".

Lints for rule polypolish (line 366, /tmp/tmpf06e0zdf/workflow/Snakefile):
    * Param path is a prefix of input or output file but hardcoded:
      If this is meant to represent a file path prefix, it will fail when
      running workflow in environments without a shared filesystem. Instead,
      provide a function that infers the appropriate prefix from the input or
      output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
      Also see:
      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
      https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions

Lints for rule busco (line 412, /tmp/tmpf06e0zdf/workflow/Snakefile):
    * No log directive defined:
      Without a log directive, all output will be printed to the terminal. In

... (truncated)

Formatting results

[DEBUG] 
[DEBUG] In file "/tmp/tmpf06e0zdf/workflow/Snakefile":  Formatted content is different from original
[INFO] 1 file(s) would be changed 😬

snakefmt version: 0.10.2