Pipelines

Collection of various bioinformatics pipelines for DNA and RNA sequencing.

Repository Structure

Pipelines for DNA sequencing and RNA sequencing tasks can be found in the sub-directories highlighted below.

.
├── DNAseq
│   ├── fastq_to_cram
│   └── fastq_to_cram_ont
├── modules
├── RNAseq
│   └── fastq_kallisto_counts
└── setup.py

Tests

Unit tests are run using pytest and can be run with the following command in the root directory.

pytest tests

Configuration for the tests can be found in the .pytest.ini configuration file. See the pytest documentation for more info.