v1.1.0

Public Health Bioinformatics v1.1.0 Release Notes

This minor release introduces two new workflows, changes the outputs for the ONT workflows, and resolves various bugs.

New workflows:

• Terra_2_GISAID
  This workflow will submit concatenated metadata and assembly files to GISAID directly from Terra. The user must obtain a GISAID client-id before they can use this workflow.

• Usher_PHB
  This workflow will place your samples onto the most up-to-date versions of the UCSC's UShER phylogenetic trees and return subtree(s) that the user can visualize.

Major output changes in TheiaCoV_ONT and TheiaProk_ONT workflows

We identified an issue when using cg_pipeline in our ONT workflows that led to inaccurate QC metrics. We have corrected this issue by deprecating the use of cg_pipeline in all ONT workflows. QC metrics are now calculated using nanoplot, which is a tool geared specifically for ONT data. In addition, since fastq-scan is now redundant in these workflows, it has been removed.

Also, the maximum read length in TheiaProk_ONT was previously set to 10,000 base pairs. We have increased this to 100,000 base pairs by default.

• TheiaProk_ONT New Outputs
  The following columns are new.

  • nanoplot_num_reads_clean1
  • nanoplot_num_reads_raw1
  • nanoplot_r1_mean_q_clean
  • nanoplot_r1_mean_q_raw
  • nanoplot_r1_mean_readlength_clean
  • nanoplot_r1_mean_readlength_raw
  • nanoplot_tsv_clean
  • nanoplot_tsv_raw
  • nanoplot_version
  • nanoplot_docker
  • nanoplot_html_clean
  • nanoplot_html_raw

  The following variables are now generated using nanoplot:

  • est_coverage_raw
  • est_coverage_clean

  The following variables have been removed:

  • num_reads_clean1
  • num_reads_raw1
  • r1_mean_q_raw
  • r1_mean_readlength_raw
  • fastq_scan_version

• TheiaCoV_ONT New Outputs
  The following columns are new.

  • nanoplot_tsv_clean
  • nanoplot_tsv_raw
  • nanoplot_version
  • nanoplot_docker
  • nanoplot_html_clean
  • nanoplot_html_raw
  • est_coverage_raw
  • est_coverage_clean
  • r1_mean_readlength_clean
  • r1_mean_readlength_raw
  • r1_mean_q_clean
  • r1_mean_q_raw

  The following variables are now generated using nanoplot:

  • num_reads_clean1
  • num_reads_raw1

  The following variables have been removed:

  • fastq_scan_version

Bug Fixes

• Corrected an inaccurate file extension in the augur workflow.
• Adjusted several files to meet the style guide
• Adjusted the default value for the core_genome input in Snippy_Tree to be true.
• Fixed a bug in the summarize_data task
• Fixed a bug and added new outputs in the SRA_Fetch workflow
• Enabled the skipping of extra header columns in the Concatenate_Column_Content workflow
• Added the .gfa file from Dragonflye as output
• Updated default docker images and dataset tags for the Pangolin and Nextclade tasks.
• Updated the GAMBIT database to v1.1.0
• The GAMBIT docker image has been updated to use the latest GAMBIT version
• Fixed a bug in file name parsing in the Lyve_Set_PHB workflow
• Skipped the genome size estimation in the read_screen task for all ONT workflows.

What's Changed

• update default docker for busco to GAR docker image by @kapsakcj in #132
• change file extension by @sage-wright in #134
• minor mashtree improvements by @kapsakcj in #142
• [TheiaProk] expose kleborate_virulence_score and kleborate_resistance_score by @cimendes in #146
• Explode workflows by @sage-wright in #135
• Usher_PHB by @sage-wright in #149
• Snippy_Tree core_genome default value by @sage-wright in #144
• summarize_data task bug fix: -z bash conditional by @kapsakcj in #153
• SRA_fetch workflow & fastq-dl task improvements by @kapsakcj in #150
• Terra_2_GISAID by @sage-wright in #148
• Skip extra headers in Concatenate_Column_Content by @sage-wright in #162
• Deprecate the use of cg_pipeline for nanoplot stats by @cimendes in #164
• Update defaults by @sage-wright in #171
• update default gambit docker by @sage-wright in #173
• lyveset fastq file parsing bugfix and other improvements by @kapsakcj in #156
• update lyveSET FASTQ parsing by @kapsakcj in #177

Full Changelog: v1.0.1...v1.1.0