0.9.3

hot fix

• issues w/ alpine base image for Singularity on cluster, fixed #133

alpha, delta etc.

• version push for pangolin and nextclade
• final report now includes the WHO names (via nextclade results)

dry run and hotfix

• dry run implementation via stub for continuous integration of poreCov
• small bug fix on json output

0.9.0 New coverageplots and min read leangth support

• implemented CoVarPlot https://github.com/Psy-Fer/CoVarPlot (thx @hoelzer )
  • removed the old coverage plot
  • using the "primer trimmed bam file" from artic as "the bam output"
• implemented new guppy version and sup model dna_r9.4.1_450bps_sup.cfg
• implemented support for rapid barcoding kit via --rapid
• min and max read length can now be used for 1200 amplicon primers (see #116 )
• some bug fixes for multi-fasta inputs that could have occurred if they have the same name 3 times or more
• some adjustments in regards to the new pangolin versions

use the --update flag to always use the most recent pangolin lineage definition available

• this is independent of poreCov releases so you don't need to wait for a new poreCov release

0.8.3 bugfix

• fixed an issue that was preventing poreCov from doing guppy cpu based bascalling

bugfix on rki output csv table

• Fixed a rare occurrence where the RKI desh upload table could break

0.8.1 small bugfix

fixed an issue on --fastq_pass overwriting some reads when using a dir containing multiple e.g. "barcode01" dirs

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

0.7.14

• update to latest pangoLEARN version

0.7.13

• added some stability improvements for summary report generation