bettercallsal v0.5.0

bettercallsal preprint is out at biorxiv.org.

This is the v0.5.0 release of bettercallsal with following changes:

• Now, fastp is used to perform quality control and adapter trimming. By default, custom adapters are not used but can be turned on with --fastp_use_custom_adapters true option.
  • The custom adapters distributed with the software will be used automatically with --fastp_use_custom_adapters true command-line option. Please note that this will make the workflow run slow due to exhaustive search for all possible adapter and primer sequences.
  • To use your own adapter FASTA, supply a valid UNIX path to --fastp_adapter_fasta command-line option.
    • Ex: --fastp_use_custom_adapters true --fastp_adapter_fasta /path/to/custom/adapters.fasta.
• Based on internal research, we found that running the workflow on concatenated R1+R2 reads yields better results if the input library is paired-end. This version of bettercallsal automatically concatenates the R1 and R2 reads if the input data set is paired-end. Use the command-line option --fq_single_end false to trigger this step.
  • Please note that you need to set the --fq_suffix and --fq_suffix2 options correctly. By default --fq_suffix is set to .fastq.gz. For paired-end, --fq_suffix may have to be set to --fq_suffix '_R1_001.fastq.gz'.
• Addition of a global Salmonella presence/absence table in the MultiQC report.
• Squashed some bugs.