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@cimendes cimendes released this 17 Jan 18:03
· 274 commits to main since this release
v1.3.0
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Public Health Bioinformatics v1.3.0 Release Notes

This minor release introduces two new workflows, improves on several workflows, and resolves various bugs

Full release notes can be found here.

🆕 New workflows:

🚀 Changes to existing workflows:

  • TheiaCoV_ONT_PHB

    • Influenza is now supported. Use "flu" for the organism optional input String parameter.
      • "sars-cov-2" and "HIV" tracks are unchanged.

  • TheiaProk Workflow Series

    • If user-input (expected_taxon) or predicted taxon by Gambit belongs to the Shigella genus, the Extensively Drug-Resistant phenotype is predicted using the new resfinder pointfinder database.
    • If user-input (expected_taxon) or predicted taxon by Gambit is the Mycobacterium tuberculosis species, bcftools indexes and merges all potential VCF files created by TbProfiler (both .bcf and .gz files).
    • Kraken2 has been added as an optional module (except for TheiaProk_ONT_PHB). If call_kraken is true, a database must be provided through kraken_db.
    • Two new optional inputs were added to control ANIm behaviour: ani_threshold (default 85.00) and percent_bases_aligned_threshold (default 70.00).

  • TheiaCoV_FASTA_PHB

    • The list of allowed input organism now includes "sars-cov-2" (default), "rsv_a", "rsv_b", "WNV", "MPXV" and "flu".

  • TheiaCoV_Illumina_PE_PHB

    • If organism is set as "flu", the workflow searches for antiviral mutations in the HA, NA, PA, PB1 and PB2 assembly segments, targeting the following 10 antivirals.: A_315675, compound_367, Favipiravir, Fludase, L_742_001, Laninamivir, Peramivir, Pimodivir, Xofluza and Zanamivir.

  • All Illumina SE and PE Workflows

    • A new optional input, read_qc, to allow the user to decide between fastq_scan and fastqc for the evaluation of read quality. The affected workflows are: TheiaCoV_Illumina_PE_PHB, TheiaCoV_Illumina_SE_PHB, TheiaProk_Illumina_SE_PHB, TheiaProk_Illumina_PE_PHB, TheiaMeta_Illumina_PE_PHB and Freyja_FASTQ_PHB.

  • CZGenEpi_Prep_PHB

    • Instead of extracting the sample_is_private_column_name and the gisaid_id_column_name columns, these columns are now generated by the program using already-provided inputs and by the new is_private Boolean variable which is used to set the value for all samples in the set. The field "GISAID ID (Public ID) - Optional" will now reflect the GISAID syntax for Virus Name.

Docker container updates:

  • AMRFinderPlus has been updated to version v3.11.20 and database 2023-09-26.1
  • tbp-parser has been updated to version 1.2.0
  • Freyja has been updated to version 1.4.8
  • ts_mlst database has been updated as of January 2024
  • Gambit has been updated to version 1.3.0, including its database files
  • Pangolin4 has been updated to version 4.3.1-pdata-1.23.1
  • IRMA has been updated to version 1.1.3

Tag updates:

  • SARS-CoV-2 Nexclade Dataset Tag has been updated to 2023-12-03T12:00:00Z

🐛 Bug fixes and small improvements:

  • kSNP3_PHB: The ksnp3_core_vcfoutput has been renamed to ksnp3_vcf_ref_genome for readability. Additionally, two new outputs are provided: ksnp3_vcf_snps_not_in_ref and ksnp3_vcf_ref_samplename.
  • TheiaProk Workflow Series: The MIDAS task was adjusted to reduce logging, and therefore the size of the log file, aiding debugging & reducing storage costs.
  • TheiaMeta_Illumina_PE_PHB: A new task Krona was added for the visualization of the Kraken2 reports.
  • Mercury_Prep_N_Batch: The excluded_samples.tsv is now printed to the execution log file, aiding debugging.
  • TheiaCoV Workflow Series: The nextclade_lineage output now populates correctly for SARS-CoV-2. Additionally, the nexclade_qc field is now exposed as an output.
  • Augur_PHB: The AUGUR refine input clock_filter_iqd has been reverted to the previous default value of 4.
  • Kraken Standalone Workflows: A new task Krona was added for the visualization of the Kraken2 reports.
  • TheiaValidate_PHB: TheiaValidate now outputs a table with validation-criteria failures only. Additionally, a new input was added that can translate different column names between tables to enable comparison.
  • TheiaCoV_ONT_PBH: If a sample fails quality check with read screening, this will no longer cause the workflow to fail. Instead, it will finish with an appropriate message.
  • Samples_To_Ref_Tree_PHB: The organism input has been renamed to nextclade_dataset_name for better clarity.
  • Various workflows: Call caching was disabled in the following workflows: BaseSpace_Fetch_PHB, Transfer_Column_Content_PHB, Assembly_Fetch_PHB, Snippy_Streamline_PHB and TheiaValidate_PHB.

What's Changed

  • updated VCF output file renaming in kSNP3 task by @kapsakcj in #207
  • reduce unnecessary logging in MIDAS task by @kapsakcj in #210
  • update default amrfinderplus docker image to v3.11.20 and db 2023-09-26.1 by @kapsakcj in #229
  • TheiaCoV_ONT_PHB Influenza Track by @jrotieno in #233
  • TheiaCoV_FASTA_Batch: TheiaCoV_FASTA, for many samples at once by @sage-wright in #238
  • Add krona task to TheiaMeta_Illumina_PE by @cimendes in #213
  • added 2 QC thresholds to ANI task to reduce false positives by @kapsakcj in #168
  • Resfinder improvements, added support for Shigella spp., added XDR Shigella prediction by @kapsakcj in #159
  • disable call caching for various workflows by @kapsakcj in #251
  • Mercury_Prep_N_Batch: print the excluded_samples.tsv and update Docker to avoid Google SDK warning by @sage-wright in #220
  • Nextclade Output Added by @DOH-HNH0303 in #239
  • TheiaCoV_FASTA: Adding five new organisms by @jrotieno in #194
  • Update task_augur_refine iqd back to 4 by @jrotieno in #268
  • TheiaCoV Illumina PE: Identify Influenza Antiviral Resistance Mutations in Assemblies by @jrotieno in #252
  • [New Utility] Workflow to rename FASTQ files (non-destructive) by @cimendes in #267
  • [TheiaCoV_Fasta_Batch] Substitute FASTA concatenating task to ensure proper sample_id propagation by @cimendes in #274
  • Kraken2 Standalone: add krona visualisation by @cimendes in #225
  • TheiaValidate_PHB: new features and new Docker image from TheiaValidate repository by @sage-wright in #255
  • TheiaProk TB: new VCF output and modification to the coverage report by @sage-wright in #245
  • TheiaCoV_ONT: prevent failure by coercing files into strings by @sage-wright in #288
  • update default freyja docker image to 1.4.8 for multiple tasks by @kapsakcj in #289
  • FastQC added as an optional module in all Illumina_PE and Illumina_SE workflows by @sage-wright in #260
  • update docker to version tag 2.23.0-2024-01 by @cimendes in #293
  • [TheiaProk Workflows] Add Kraken2 as optional module by @cimendes in #286
  • CZGenEpi_Prep_PHB: implementing user-requested changes by @sage-wright in #244
  • Update Gambit database files to version 1.3.0 by @kevinlibuit in #292
  • [PHB Release 1.3.0] update version and docker tags (nexclade sc2, pangolin, tbp-parser 1.1.7) by @cimendes in #296
  • [PR Template Update] Updating template per identified dev process improvements by @kelseykropp in #300
  • [TheiaProk suite] Patch fix: change type of kraken2_report to be string in taxon_table task by @cimendes in #297
  • Samples_To_Ref_Tree_PHB: changed "organism" input to "nextclade_dataset_name" by @jrotieno in #303
  • theiacov_fasta wf logic change for flu by @kapsakcj in #305
  • restore vadr_num_alerts string output to theiacov_fasta workflow by @kapsakcj in #307

New Contributors

Full Changelog: v1.2.1...v1.3.0

Contributors

kapsakcj, cimendes, and 5 other contributors
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