[1.1.0] - 2020-06-23 Added #112 - Per-amplicon coverage plot #124 - Intersect variants across callers #118 Updated GitHub Actions AWS workflow for small and full size tests. nf-core/tools#616 - Updated GitHub Actions to build Docker image and push to Docker Hub Parameters: --min_mapped_reads to circumvent failures for samples with low number of mapped reads --varscan2_strand_filter to toggle the default Varscan 2 strand filter --skip_mosdepth - skip genome-wide and amplicon coverage plot generation from mosdepth output --amplicon_left_suffix - to provide left primer suffix used in name field of --amplicon_bed --amplicon_right_suffix - to provide right primer suffix used in name field of --amplicon_bed Unify parameter specification with COG-UK pipeline: --min_allele_freq - minimum allele frequency threshold for calling variants --mpileup_depth - SAMTools mpileup max per-file depth --ivar_exclude_reads renamed to --ivar_trim_noprimer --ivar_trim_min_len - minimum length of read to retain after primer trimming --ivar_trim_min_qual - minimum quality threshold for sliding window to pass --ivar_trim_window_width - width of sliding window Removed --skip_qc parameter Dependencies Add mosdepth 0.2.6 Add bioconductor-complexheatmap 2.2.0 Add bioconductor-biostrings 2.54.0 Add r-optparse 1.6.6 Add r-tidyr 1.1.0 Add r-tidyverse 1.3.0 Add r-ggplot2 3.3.1 Add r-reshape2 1.4.4 Add r-viridis 0.5.1 Update sra-tools 2.10.3 -> 2.10.7 Update bowtie2 2.3.5.1 -> 2.4.1 Update picard 2.22.8 -> 2.23.0 Update minia 3.2.3 -> 3.2.4 Update plasmidid 1.5.2 -> 1.6.3