nf-core/viralrecon v1.1.0 - Steel Pangolin

[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