Changes in this release:
- Singularity container support for all rules. In fact, singularity is now the preferred method of executing the pipeline. This allows much better isolation of run environments.
- Versions of tools are the same as in the (now legacy) conda environments, bar one: fastqc. When using singularity, fastqc uses version 0.11.7, as opposed to version 0.11.5 when using conda. The differences are minor, with the largest difference being that the per-tile statistics for Novaseq runs only work on 0.11.7.
- Gather steps now use bcftools in stead of GATK's CatVariants. This is considerably faster, and less memory-intensive.