cfusterot/sodar

SODAR

This snakemake pipeline aims at facilitating the uploading of samples to the SODAR platform.

Authors

• Coral Fustero-Torre

Setup

For setting up the pipeline, three configuration files need to be modified. See the Usage section for more details.

Configuration files

• config.yaml contains all pipeline parameters.
• samples.tsv: contains metadata annotations. An example file can be downloaded, have in mind not all columns will be necessary.

Usage

1. Set up the environment

SODAR requires the installation of the conda package manager in order to work. Please install conda by following the bioconda installation instructions. In addition, it is essential to install Snakemake; following the steps in the Snakemake documentation.

To run the pipeline, the user needs to create the conda environments first, which will take some minutes. This step is done automatically using the following command:

snakemake --use-conda --conda-create-envs-only --conda-frontend mamba

2. Download the SODAR repository from Github.

Use git clone command to create a local copy.

git clone https://github.com/cfusterot/SODAR.git

3. Configure the pipeline.

Before executing the pipeline, the users must configure it according to their samples.

a. config.yaml

This is the pipeline configuration file, where you can tune all the available parameters to customise the uploading of the samples. An example file (config-example.yaml) is included in the repository. Rename it to config.yaml and edit its contents.

Field name	Description
samples	Path to the samples.tsv file
out	Path to output location
log	Path to log files location
input_dir	Path to FASTQ file folder
sample_id	Sample unique identifier
landing_dir	Path to landing directory

c. samples.tsv

This table contains the name of each sample and the experimental condition it belongs to.

An example file (samples-example.tsv) is included in the repository. Rename it to samples.tsv and edit its contents. Mandatory columns include:

• scATAC-seq samples
• ID
• Lab Register ID
• Date
• primer

4. Run the pipeline.

Once the pipeline is configured and conda environments are created, the user just needs to run iSODAR as follows:

snakemake --use-conda --jobs 3

The mandatory arguments are:

• --use-conda: to install and use the conda environemnts.
• -j: number of threads/jobs provided to snakemake.