version 3.1.0 --------------------------- + Default threads for BWA in bwa.Kit task: 4. Samtools sort in the same task: 1. Output BAM compression level to 1. + Lima: Add missing output to parameter_meta. + Lima: Remove outputPrefix variable from output section. + Isoseq3: Make sure stderr log file from Refine is unique and not overwritten. + Isoseq3: Add workaround in Refine for glob command not locating files in output directory. + Isoseq3: Fix --min-polya-length argument syntax. + Lima: Add workaround for glob command not locating files in output directory. + CCS: Add missing backslash. + Cutadapt now explicitly calls the `--compression-level` flag with compression level 1 to prevent cutadapt from using very high gzip compression level 6 that uses 400% more cpu time. + Update default docker image for cutadapt and fastqc. + Default number of cores for cutadapt and bwamem to 4 cores.