1.5.0

Increased phred threshold in ConfindR analysis of Illumina data from Q20 to Q25 to remove false positive contaminations reported to otherwise occur on current generaton Illumina instruments
Removed Nanopore ConfindR as a fail category from final sample classification due to occurences of false contamination calls
Combined serotyping results from ECTper and Abricate EcOH in the final HTML report as neither tool alone seems to do well on benchmark data
Removed option to filter reads against host genome due to aggressive license restrictions of biobloomtools as well as unpredictable effects on downstream applications

1.4.2

Added an upper version lock to the pipeline, preventing execution with new and untestet versions of nextflow
Fixed an issue with Plassembler database installation
Updated autocycler to 0.6.2

Updated reference database to v1.2
Added Autocycler to optionally run consensus assembly for long reads
Added Plassembler to default long-read assembly workflows to improve recovery of plasmids when not using Autocycler
Moved redundant genome size calculations into its own sub workflow
Defaulting genome size estimate to 6MB if calculation fails
Medaka polishing: Check if reads contain basecalling model meta data; else skip if model isn't provided via command line
Replaced ConfindR db download with proper installation workflow
Updated CheckM2 database download to specify a user-agent as a fix to aborting file transfers
Adding pipeline settings to sample-level JSON
Updated Chopper to version 0.12.0