Release 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.