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nf-core/viralrecon: nf-core/viralrecon v1.1.0 - Steel Pangolin

Harshil Patel; Sarai Varona; Sara Monzón; Jose Espinosa-Carrasco; Michael L Heuer; Gisela Gabernet; MiguelJulia; Stephen Kelly; Katrin Sameith; Maxime Garcia; jcurado

[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

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