Test dataset

This test dataset is used for testing the silol-nanopore-coe/nanoabo pipeline. It contians 3 folders as follows:

1. samplesheets - this folder contains samplesheet CSV files for the test config.
2. sample_info - this folder contains the sample information CSV file for the test config.
3. clair3_model - this folder contains the clair3 model used for the test dataset.

The paths to the samplesheet and sample information files are provided in the pipeline and automatically downloaded when running the pipeline with the test profiles.

Download the Clair3 model

Because the Clair3 model is not integrated in the pipeline, users must download the Clair3 model beforehand and provide it to the pipeline. To download the model for testing, you run the following command:

# Create the directory where the model will be saved
mkdir clair3_model

# Change to the created directory
cd clair3_model

# Downlod the model
wget https://github.com/ArissaraT/test-dataset/raw/refs/heads/main/clair3_model/r1041_e82_400bps_sup_v420.tar.gz

# Uncompress tar file
tar -xzvf r1041_e82_400bps_sup_v420.tar.gz

The model folder should contain the files that look like this:

clair3_model/
└── r1041_e82_400bps_sup_v420
    ├── full_alignment.data-00000-of-00001
    ├── full_alignment.index
    ├── pileup.data-00000-of-00001
    └── pileup.index

For usage docs, see the silol-nanopore-coe/nanoabo pipeline.