richardstoeckl/basecallNanopore

Snakemake Pipeline to automatically basecall Nanopore sequencing data with hybrid approach of simplex and duplex basecalling

Overview

Topics:

Latest release: v1.0.2, Last update: 2024-05-27

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/basecallNanopore . --tag v1.0.2

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 according to your needs, following the explanations provided in the file.

"Main" section

Here you should provide the paths to your intermediary/results/logs directories. The interim directory will contain larger intermediary files. The results directory will contain the final output of the pipeline. The logdirectory will be used to store the log files for each step. Here you should also write the name of your run file (see relevant section below).

"Tools" section

Here you should give the paths to your guppy and/or dorado installation. Additionally you should change the given parameters to suit your compute setup.

Run file setup

The setup of the basecall runs is specified via comma-separated values files (.csv). Missing values can be specified by empty columns.

Depending on what you enter here, the pipeline will automatically adjust what will be done (e.g. which basecaller will be used and how many barcodes will be used).

You can use the config/runs_test.csvfile as a template.

Linting and formatting

Linting results

Lints for snakefile /tmp/tmpmxvhfajh/richardstoeckl-basecallNanopore-8d272b1/workflow/rules/basecall.smk:
    * Absolute path "/{barcode}_readIDs.txt" in line 320:
      Do not define absolute paths inside of the workflow, since this renders
      your workflow irreproducible on other machines. Use path relative to the
      working directory instead, or make the path configurable via a config
      file.
      Also see:
      https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
    * Mixed rules and functions in same snakefile.:
      Small one-liner functions used only once should be defined as lambda
      expressions. Other functions should be collected in a common module, e.g.
      'rules/common.smk'. This makes the workflow steps more readable.
      Also see:
      https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes

Lints for rule guppy_simplex (line 34, /tmp/tmpmxvhfajh/richardstoeckl-basecallNanopore-8d272b1/workflow/rules/basecall.smk):
    * Specify a conda environment or container for each rule.:
      This way, the used software for each specific step is documented, and the
      workflow can be executed on any machine without prerequisites.
      Also see:

... (truncated)

Formatting results

[DEBUG] 
[DEBUG] 
[DEBUG] In file "/tmp/tmpmxvhfajh/richardstoeckl-basecallNanopore-8d272b1/workflow/rules/basecall.smk":  Formatted content is different from original
[DEBUG] 
[INFO] 1 file(s) would be changed 😬
[INFO] 2 file(s) would be left unchanged 🎉

snakefmt version: 0.10.2