zenodo release

Merge pull request #11 from bge-barcoding/main

Merging updates

publication-release

Release in line with BeeGees version used in publication.

v2.0.0

• Numerous QoL fixes
• Increased flexibility of pre-processing rules to enable more graceful handling of empty input files, including placeholder file creation
• Addition of pre-barcode recovery decontamination rules
• Enhancement of human COI filtering based on sequence similarity, to human mitogenome mapping using BWA-aln
• Statistics compilation script enhancements, in line with new decontaminantion steps and human mitogenome filtering

v1.1.0

Main changes:

• Separation of downsampling from initial fastp QC step(s) using fastp's reads_to_process argument, and refactoring of pre-processing to include optional downsampling (using BBTools reformat.sh) after initial QC.
• Inclusion of barcoding_outcome.py (and associated 05_barcoding_outcome/ results directory) to provide an overview of barcoding success (PASS/PARTIAL/FAIL) for each processed sample.
• Minor QoL improvements and filename changes.

v1.0.0

v1.0.0 release of BGEE pipeline, including read preprocessing, pseudo-reference searching (gene fetch), barcode recovery (MGE), consensus sequence cleaning (fasta_cleaner), and barcode validation (structural and taxonomic).