Add krona task to TheiaMeta_Illumina_PE

[cimendes]

Closes

🛠️ Changes Being Made

This PR adds new functionality to TheiaMeta: Krona Charts

Krona allows hierarchical data to be explored with zooming, multi-layered pie charts.

On Terra, an HTML file is populated on the datatable that can be downloaded and explored on the browser interactively for both raw and read screen taxonomic assessment.

🧠 Context and Rationale

Krona allows for the interactive visualization of the entire community at a high level. It also allows for to drill down for taxa of interest, keeping the taxonomic relationships.

📋 Workflow/Task Steps

Inputs

N/A

Outputs

4 new outputs have been added to TheiaMeta:

    String krona_version = krona_raw.krona_version
    String krona_docker = krona_raw.krona_docker
    File krona_html_raw = krona_raw.krona_html
    File krona_html_clean = krona_clean.krona_html

🧪 Testing

Locally

Tested locally with miniwdl, both at the task level and the entire TheiaMeta workflow

2023-10-11 09:04:27.829 wdl.w:theiameta_illumina_pe done
{
  "dir": "/home/ines_mendes/WDL/20231011_083247_theiameta_illumina_pe",
  "outputs": {
    "theiameta_illumina_pe.assembly_fasta": "/home/ines_mendes/WDL/20231011_083247_theiameta_illumina_pe/out/assembly_fasta/HAV0024.fasta",
    "theiameta_illumina_pe.assembly_length": 7499,
    "theiameta_illumina_pe.assembly_mean_coverage": 2436.59,
    "theiameta_illumina_pe.average_read_length": 157.0,
    "theiameta_illumina_pe.bbduk_docker": "us-docker.pkg.dev/general-theiagen/staphb/bbtools:38.76",
    "theiameta_illumina_pe.bedtools_docker": "us-docker.pkg.dev/general-theiagen/staphb/bedtools:2.31.0",
    "theiameta_illumina_pe.bedtools_version": "v2.31.0",
    "theiameta_illumina_pe.contig_number": 1,
    "theiameta_illumina_pe.fastq_scan_docker": "quay.io/biocontainers/fastq-scan:0.4.4--h7d875b9_1",
    "theiameta_illumina_pe.fastq_scan_version": "fastq-scan 0.4.4",
    "theiameta_illumina_pe.kraken2_docker": "us-docker.pkg.dev/general-theiagen/staphb/kraken2:2.1.2-no-db",
    "theiameta_illumina_pe.kraken2_percent_human_clean": 24.04,
    "theiameta_illumina_pe.kraken2_percent_human_raw": 68.11,
    "theiameta_illumina_pe.kraken2_report_clean": "/home/ines_mendes/WDL/20231011_083247_theiameta_illumina_pe/out/kraken2_report_clean/HAV0024.report.txt",
    "theiameta_illumina_pe.kraken2_report_raw": "/home/ines_mendes/WDL/20231011_083247_theiameta_illumina_pe/out/kraken2_report_raw/HAV0024.report.txt",
    "theiameta_illumina_pe.kraken2_version": "2.1.2",
    "theiameta_illumina_pe.krona_docker": "us-docker.pkg.dev/general-theiagen/biocontainers/krona:2.7.1--pl526_5", <---
    "theiameta_illumina_pe.krona_html_clean": "/home/ines_mendes/WDL/20231011_083247_theiameta_illumina_pe/out/krona_html_clean/HAV0024_krona.html",  <--- 
    "theiameta_illumina_pe.krona_html_raw": "/home/ines_mendes/WDL/20231011_083247_theiameta_illumina_pe/out/krona_html_raw/HAV0024_krona.html",  <---
    "theiameta_illumina_pe.krona_version": "2.7.1", <---
    "theiameta_illumina_pe.largest_contig": 7499, 
    "theiameta_illumina_pe.metaspades_docker": "us-docker.pkg.dev/general-theiagen/biocontainers/spades:3.12.0--h9ee0642_3",
    "theiameta_illumina_pe.metaspades_version": "v3.12.0",
    "theiameta_illumina_pe.minimap2_docker": "us-docker.pkg.dev/general-theiagen/staphb/minimap2:2.22",
    "theiameta_illumina_pe.minimap2_version": "2.22-r1101",
    "theiameta_illumina_pe.ncbi_scrub_docker": "us-docker.pkg.dev/general-theiagen/ncbi/sra-human-scrubber:1.0.2021-05-05",
    "theiameta_illumina_pe.num_reads_clean1": 246155,
    "theiameta_illumina_pe.num_reads_clean2": 246155,
    "theiameta_illumina_pe.num_reads_clean_pairs": "246155",
    "theiameta_illumina_pe.num_reads_raw1": 1607300,
    "theiameta_illumina_pe.num_reads_raw2": 1607300,
    "theiameta_illumina_pe.num_reads_raw_pairs": "1607300",
    "theiameta_illumina_pe.percent_coverage": 99.08,
    "theiameta_illumina_pe.percentage_mapped_reads": 21.0312,
    "theiameta_illumina_pe.pilon_docker": "us-docker.pkg.dev/general-theiagen/biocontainers/pilon:1.24--hdfd78af_0",
    "theiameta_illumina_pe.pilon_version": "1.24",
    "theiameta_illumina_pe.quast_docker": "us-docker.pkg.dev/general-theiagen/staphb/quast:5.0.2",
    "theiameta_illumina_pe.quast_version": "QUAST v5.0.2",
    "theiameta_illumina_pe.read1_clean": "/home/ines_mendes/WDL/20231011_083247_theiameta_illumina_pe/out/read1_clean/HAV0024_1.clean.fastq.gz",
    "theiameta_illumina_pe.read1_dehosted": "/home/ines_mendes/WDL/20231011_083247_theiameta_illumina_pe/out/read1_dehosted/HAV0024_R1_dehosted.fastq.gz",
    "theiameta_illumina_pe.read1_mapped": "/home/ines_mendes/WDL/20231011_083247_theiameta_illumina_pe/out/read1_mapped/assembled_HAV0024_1.fq.gz",
    "theiameta_illumina_pe.read1_unmapped": "/home/ines_mendes/WDL/20231011_083247_theiameta_illumina_pe/out/read1_unmapped/unassembled_HAV0024_1.fq.gz",
    "theiameta_illumina_pe.read2_clean": "/home/ines_mendes/WDL/20231011_083247_theiameta_illumina_pe/out/read2_clean/HAV0024_2.clean.fastq.gz",
    "theiameta_illumina_pe.read2_dehosted": "/home/ines_mendes/WDL/20231011_083247_theiameta_illumina_pe/out/read2_dehosted/HAV0024_R2_dehosted.fastq.gz",
    "theiameta_illumina_pe.read2_mapped": "/home/ines_mendes/WDL/20231011_083247_theiameta_illumina_pe/out/read2_mapped/assembled_HAV0024_2.fq.gz",
    "theiameta_illumina_pe.read2_unmapped": "/home/ines_mendes/WDL/20231011_083247_theiameta_illumina_pe/out/read2_unmapped/unassembled_HAV0024_2.fq.gz",
    "theiameta_illumina_pe.samtools_docker": "us-docker.pkg.dev/general-theiagen/staphb/samtools:1.17",
    "theiameta_illumina_pe.samtools_version": "1.17",
    "theiameta_illumina_pe.theiameta_illumina_pe_analysis_date": "2023-10-11",
    "theiameta_illumina_pe.theiameta_illumina_pe_version": "PHB v1.2.0",
    "theiameta_illumina_pe.trimmomatic_docker": "us-docker.pkg.dev/general-theiagen/staphb/trimmomatic:0.39",
    "theiameta_illumina_pe.trimmomatic_version": "Trimmomatic 0.39"
  }
}

Terra

Underway
21 blood samples containing DENV: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/e59ebd75-006d-4c29-82be-bda2d4ed0b15

🔬 Quality checks

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The workflow/task has been tested locally and on Terra
• The CI/CD has been adjusted and tests are passing
• Everything follows the style guide

[sage-wright]

Testing here: https://app.terra.bio/#workspaces/cdc-terra-resources/Theiagen_Wright_SC2_Sandbox/job_history/9b1b1626-dcbe-4586-9b16-14960c0ec81b

[sage-wright]

will squish once tests succeed!

[sage-wright]

Well done!