0.7.1 bugfixes, report improvements and clean ups

• Report % of Ns #66
• number of reads that are classified #62
• indel positions are reported #65
• reduced kraken footprint on server #59
• renamed --dir to --fast5 2d2e2d7
• renamed --fastq_raw to --fastq_pass 2d2e2d7
• --help updated and Readme updates

0.7.0 Major report update and various fixes extensions

• poreCov generates a nice and clean HTML report across your run
• multifasta support for the --fasta flag
• various tool version updates
• --rki produces "desh compatible" output (for upload to the desh portal)
• dag chart update to reflect what poreCov is doing
• [missing] readme cleanup

also thanks @RaverJay for the nice report file

0.6.1 fixes and updates

• bugfixes on kraken DB
• remove tree build
• update dag chart
• add alternative kraken db download on "error retry"
• update on Readme
• added nextclade mutations to json output (for mongo DB)
• improved cpu handling and help on local usage
• simplified work dir and database "dirs"
• pangolin version bump

0.6.0 read classification and nextclade

• kraken2 classification for reads + krona plot (to check for contamination and amount of stars reads)
• nextclade added, informs about clade mutations etc.

0.5.0 - lots of bug fixes and version updates

• --samples allows for sample renaming
• updates on president artic pangolin
• inclusion of most recent president to reflect quality statements

fixing some rki output bugs

Merge pull request #32 from replikation/dev_replikation

Dev replikation

0.4.1

• added correct configuration for GPU Guppy using Singularity

0.4.0 president for genome quality, and more

• code overhaul and bug fixing for upcoming additions
  • next features will be clean user reports
• error strategy for cloud computing
• cloud computing compatible für google cloud life science
• workflow abstraction to allow for bigger workflow
• president (rki) inclusion

0.3.9

• added NanoPlot for fast fastq input QC
• added president for some consensus QC (pairwise sequence identity to Wuhan strain and check for NNNN and length)
• write out BAM file from coverage calculation step for further downstream analyses

small bug fixes / typos

0.3.8

nz fix