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 to cg_process_project (uses project_make internally) (issue derijkp/scywalker#3)
• Improvement help
• Added cg error_report for easier checking of errors after a distributed run (issue derijkp/scywalker#5 and derijkp/scywalker#4)

Distribution and installation

• Added cg install for easier install of supporting binaries and refdbs
• 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

Updates of the reference databases (hg38)

• dbsnp 155
• gnomad 4.1
• gencode 45, ...

more cram support:

• cram can be used with ont presets (use -aliformat cram)
  • fix remora: modkit has problems with cram -> temp convert to bam to run
  • scywalker_report_job: support cram
• cg tsv2sam now supports -outformat cram

falco replaces fastqc
falco is a (mostly) drop-in replacement that is faster, smaller and comes with less dependencies than fastqc

Optimization cg select summaries

• by default making summaries (-g option) memory is proportional to size of output
  (other queries are independent of size)
• added option -optim memory
  • minimize memory use when making summaries with option -g
  • Using the option is slower, so do not use when (typically) small summary output is expected
  • 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)

Other changes

• Added extra cluster support (options -submitoptions, -dqueue, help, ...) (issue #1)
• process_project option -jobsample now allows specification of number of cores to be used by one-job sample analysis
• cg_cat: added option -fullfilename
• Changed preset_ont: removed npinv from default svcallers (as it often caused problems with newer data)
• cg fixtsv will also fix duplicate fields in tsv file

Full Changelog: 0.108.0...0.109.0