0.8.0 New features and improvments

pangolin

• poreCov has now a --update flag which searches for the most recent pangolin version on dockerhub (#103)
  • this means you don't need to wait for a new poreCov release that updates pangolin
  • (behind the scenes) we set up a cron job that tries to build a version-controlled pangolin every other day and pushes this to docker hub if it works without errors and contains all the data that poreCov needs
  • as this feature might break the workflow it's deactivated by default to ensure stability
• pangolin version and pangoLEARN version are now shown on the final report for better reproducability

other inclusions and bugfixes

• supporting rapid barcode kits (RBK004) add --rapid to the poreCov command
• automatically start demultiplexing on --fastq_pass input if no barcodes are detected #100
• bugfix: slurm profile was not a valid executed - now fixed, thx @KevinMenden #112
• slightly changed output-dir name, see #111
• included a new result dir 5.Genome-primer-repair which tells you which V3 or V1200 primers are needed to amplify only regions with ambiguous bases (to improve genome quality) - still a beta feature - feel free to report issues
• improved CPU handling on guppy #ec77d43
• bugfix: removing reads that are too small was not working correctly (did not effected results, but still - its fixed now) #a9a81a1
• Added more error code for the user if e.g. not enough reads are available or no genomes were reconstructed
  • this also points you to the read directory to check on e.g. how many barcodes you have or reads that are viral
• some visual updates on the final output report