baitcapture - v2.0.0 'Victoria'

This release of BaitCapture improves greatly upon v1.0.0, with several added features including: - Custom alignment and summary statistics report tables, which are outputted to a summary/ directory - Ability to define thresholds for target detection on the command-line - Ability to provide a target metadata file on the command-line for cluster-level detection - Option to report all undetected targets in outputs - KMA as a new (and default) aligner - fastp for adapter removal and read trimming - Mosdepth for a nice overview of read alignments in the MultiQC report

- Nextflow
Published by pcrxn almost 2 years ago

baitcapture - 1.0.0

What's Changed

• First draft of workflow by @pcrxn in https://github.com/OLC-Bioinformatics/BaitCapture/pull/1
• Add Conda, Docker, and Singularity as options for package management by @pcrxn in https://github.com/OLC-Bioinformatics/BaitCapture/pull/2
• Add kma as an alignment tool by @pcrxn in https://github.com/OLC-Bioinformatics/BaitCapture/pull/3
• Add host decontamation by @pcrxn in https://github.com/OLC-Bioinformatics/BaitCapture/pull/4
• Use BWA-MEM2 for host decontamination by @pcrxn in https://github.com/OLC-Bioinformatics/BaitCapture/pull/5
• Subworkflow refactor by @pcrxn in https://github.com/OLC-Bioinformatics/BaitCapture/pull/6
• Refactor code by @pcrxn in https://github.com/OLC-Bioinformatics/BaitCapture/pull/7
• Add kma as an optional aligner by @pcrxn in https://github.com/OLC-Bioinformatics/BaitCapture/pull/8
• Add bwa mem by @pcrxn in https://github.com/OLC-Bioinformatics/BaitCapture/pull/9
• v1.0.0_dev by @pcrxn in https://github.com/OLC-Bioinformatics/BaitCapture/pull/10

New Contributors

• @pcrxn made their first contribution in https://github.com/OLC-Bioinformatics/BaitCapture/pull/1

Full Changelog: https://github.com/OLC-Bioinformatics/BaitCapture/commits/1.0.0

- Nextflow
Published by pcrxn over 2 years ago