CheckCDS

CheckCDS is a compi pipeline to produce valid CDS files. A Docker image is available for this pipeline in this Docker Hub repository.

CheckCDS repositories

• GitHub
• DockerHub
• CompiHub

Using the CheckCDS image in Linux

In order to use the CheckCDS image, you should run and adapt the following command:

docker run --rm -v /path/to/input:/input -v /path/to/output:/output pegi3s/check-cds -- -r <reference_sequence>

Where you should replace:

• /path/to/input to point to the directory that contains the input file you want to process.
• /path/to/output to point to the directory where the output files must be created.
• <reference_sequence> to the string that must be found in the reference sequence (case insensitive).

By default, a maximum of 6 parallel tasks can be run. To modify this value, use the --num-tasks parameter as the following example shows (replacing <num_tasks> with the new value):

docker run --rm -v /path/to/input:/input -v /path/to/output:/output pegi3s/check-cds --num-tasks <num_tasks> -- -r <reference_sequence>

Test data

The sample data is available here. Download the FASTA files and put them inside a directory named check_cds_test_data in your local file system.

Then, you should adapt and run the following command:

docker run --rm -v /path/to/check_cds_test_data:/input -v /path/to/output:/output pegi3s/check-cds -- -r seq4

Building the Docker image

To build the Docker image, compi-dk is required. Once you have it installed, simply run compi-dk build from the project directory to build the Docker image. The image will be created with the name specified in the compi.project file (i.e. pegi3s/check-cds:latest). This file also specifies the version of compi that goes into the Docker image.

References

• H. López-Fernández; C. P. Vieira; P. Ferreira; P. Gouveia; F. Fdez-Riverola; M. Reboiro-Jato; J. Vieira (2021) On the identification of clinically relevant bacterial amino acid changes at the whole genome level using Auto-PSS-Genome. Interdisciplinary Sciences: Computational Life Sciences. Volume 13, pp. 334–343.