0.109.0

Major changes are:

Qol improvements

• added cg project_make for creating a basic experiment/project directory based on a samplesheet
• Added option -samplesheet for creating a basic experiment/project directory based on a samplesheet (issue #3)
• Improvement help
• Added cg error_report for easier checking of errors after a distributed run (issue #5 and #4)

Distribution and installation

• include more dependencies in distro (from testing in minimal docker distro)
  • less, which, bzcat, bzip2, dot
  • extra libs for dirR
  • semi-static compiles of samtools, bgzip, tabix

cram support:

• cram can be used using the option -aliformat cram

Optimization cg select summaries

• added option -optim memory to minimize memory use when making summaries using cg select with the -g option
  (default memory is proportional to size of summary output)
• used in scywalker for getting aggregate data from sc_gene and sc_isoforms

Optimizations (esp. for starting big runs)

• file access optimizations (check for compressed only where specified, direct deps check, use cached data)
• storage optimizations (shadowdirs)
• jobs optimizations (integrate cleanup, merge jobs, hold_jid in runfile)

Ohter changes

• Added extra cluster support (options -submitoptions, -dqueue, help, ...)
• process_project option -jobsample now allows specification of number of cores to be used by one-job sample analysis

Full Changelog: v0.108.0...0.109.0