Release 0.2.3

🚀 Improvements & Fixes

🐛 Bug Fixes

• Fixed an issue in Kraken2 where single-end sequence handling had minor errors.
• Resolved a bug that caused a highlighting error if genome_path was not set and --use_kneaddata was set to false.

🛠️ FASTP Processing Enhancements

• Enabled automated adapter detection for paired-end (PE) reads.
• Skipped duplication evaluation, considering the low diversity of amplicon libraries.
• Enabled read correction in PE overlaps, requiring a minimum overlap of 20 nt.
• Activated read discarding for:
  • PE reads shorter than 50 nt
  • Single-end (SE) reads shorter than 100 nt

This update improves overall stability and preprocessing efficiency for sequencing data

Minor bug fixes and improvements for Nextflow release

• Added support for the sequences file name in format SampleID_S20_L001_R1_001.fastq + SampleID_S20_L001_R2_001.fastq for paired-end reads. Reads in fomat SampleID_1.fastq + SampleID_2.fastq are preferred.
• Fixed issues in path binding with the singularity container

Nextflow release

In the 16s-krakenbracken-pipeline-v2.tar.gz archive you will find:

• nextflow.config config file
• kraken16S.nf script for launching nextflow

Extract the archive where you want and add the 16s-krakenbracken-pipeline folder to ${PATH} to enable calling the pipeline from elsewhere in your machine.
Alternatively, a .zip archive is available as well. You can also find the nextflow.config and kraken16S.nf files in the main branch of this repo.