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@frankambrosio3 frankambrosio3 released this 23 Oct 20:19
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v1.2.1
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Public Health Bioinformatics v1.2.1 Release Notes

This patch release resolves various bugs and updates workflow defaults.

🐛 Bug Fixes

🦑 Kraken2_PE

  • A bug was fixed in the Kraken2_PE_PHB standalone workflow where the workflow was expecting required outputs from the Kraken2_standalone task that are now optional. This solves the issue encountered when trying to import the workflow which would be unsuccessful.

Impacted Workflows/Tasks:

  • Kraken2_PE_PHB

The following workflows uses Kraken2_standalone task but have not been affected as they do not require the affected outputs:

  • TheiaMeta_Illumina_PE_PHB
  • Kraken2_SE_PHB

The following workflows use a different Kraken2 task and have not been affected:

  • TheiaCoV_Illumina_PE_PHB
  • TheiaCoV_Illumina_SE_PHB

🌲 Augur

  • The requirement to present genes and colors input files was causing run failures for non-MPXV tree builds. These files are no long required.

Users reported issues with with optional Augur_PHB inputs, specifically colors_tsv, with the following error messages:

  • Error_1:"Failed to evaluate 'colors_tsv' (reason 1 of 1): Evaluating select_first([colors, mpxv_defaults.colors]) failed: select_first was called with 2 empty values. We needed at least one to be filled."
  • Error_2: "Failed to evaluate 'genes' (reason 1 of 1): Evaluating select_first([genes, mpxv_defaults.genes]) failed: select_first was called with 2 empty values. We needed at least one to be filled."

📚 Read Screen

  • The read screen task is designed to assess the quantity and quality of reads used as the input to the workflow, and halt the workflow if it is determined that the reads are insufficient. One of the qualities of the reads that is checked is the proportion of reads found in the R1 and R2 files.
    • The former implementation did not calculate the proportion of reads correctly, and the reported error message did not reflect the defined parameter correctly.
    • The math has been updated such that the ratio can not be unbalanced beyond a 60/40 split.

🔧 Workflows Updates

Workflows

🔬 TheiaCoV Workflows

  • The default nextclade_dataset_tag for SARS-CoV-2 was updated to "2023-09-21T12:00:00Z" (as of 2023-10-10) across all 5 TheiaCov workflows:
    • TheiaCoV_Illumina_PE_PHB, TheiaCoV_Illumina_SE_PHB, TheiaCoV_ClearLabs_PHB, TheiaCoV_ONT_PHB, TheiaCoV_FASTA_PHB

🦠 TheiaProk Workflows

  • KmerFinder was added to the TheiaProk suite of workflows to find the best match (species identification) of a fasta file in a (kmer) database (downloaded on 2023-09-11).
New Outputs
  • kmerfinder_docker
  • kmerfinder_results_tsv
  • kmerfinder_top_hit
  • kmerfinder_query_coverage
  • kmerfinder_template_coverage
  • kmerfinder_database

Task Files

🎙️ UShER

  • The runtime environment for the UShER task has been allocated additional compute resources to allow for larger input sets.
  • The following defaults for the Pilon task were changed:
    • CPU 4 -> 8
    • Memory 8 -> 32
  • Impacted Workflows/Tasks
    • UShER _PHB is the only affected workflow.

🔎 Pilon

  • The runtime environment for the Pilon task has been allocated additional compute resources to allow for larger input sets.
  • The following defaults for the Pilon task were changed:
    • CPU 4 -> 8
    • Memory 8 -> 32
  • Impacted Workflows/Tasks
    • TheiaMeta_Illumina_PE_PHB is the only affected workflow.

🏭 What's Changed

Full Changelog: v1.2.0...v1.2.1

Please see the full documentation for the PHB repository v1.2.1 release.

Contributors

kapsakcj, cimendes, and 2 other contributors
Assets 2
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