BACTpipe v3.1.0

Notable changes in version 3.1.0:

• Replaced Sendsketch-based contamination screening step with Kraken2 taxonomic profiling
• Now publishes shovill.log in the output directory by default.
• Added new profiles for use with Docker and CTMR Slurm HPC system Gandalf.

For more details, refer to the CHANGELOG.

BACTpipe v2.7.0

Check CHANGELOG for notable changes.

Zenodo v2.6.0

This is release is to provide a citable Zenodo DOI for BACTpipe v2.6.0

BACTpipe v2.6.0

First public release

This is the first truly public release of BACTpipe implemented in Nextflow. This is the first official release, and is considered fairly reliable. Development will continue in the develop branch, and the master branch will from now on only receive major updates and potentially hotfixes.

Try it out and let us know what you think!

nextflow run ctmrbio/BACTpipe --reads 'path/to/*_R{1,2}.fastq.gz' 

Check the official documentation at https://bactpipe.readthedocs.org for more details on requirements and how to run BACTpipe.

BACTpipe first internal release

v1

Fixed typo