expose bwa mem -T parameter

[ivokwee]

Hi. I had a case that I needed to lower the score threshold of BWA-mem. The default is T=30 but all reads were filtered out and I had to set the T=15. Can we expose the T option in the nextflow run options?

[drpatelh]

Hi @ivokwee. Sounds like a reasonable request. Was there a reason as to why the alignments had low scores? We could either add a generic parameter e.g. --alignment_options or a specific one to tweak that particular option e.g. --alignment_score. Using the former would be much easier to integrate with Nextflow DSL 2 which is not far off now for this pipeline.

[drpatelh]

Fixed here @ivokwee. Thanks for reporting!