[TheiaEuk] TheiaEuk ONT Workflow

[Michal-Babins]

This PR closes #625

🗑️ This dev branch should be deleted after merging to main.

🧠 Summary

Creates a TheiaEuk workflow for ONT reads

⚡ Impacted Workflows/Tasks

• New workflow: wf_theiaeuk_ont
• Modified: wf_merlin_magic (to accommodate eukaryotic-specific analyses)
• Modified: task_snippy_variants and task_snippy_gene_query (to work with ONT data)
• Modified: wf_read_QC_trim_ont for theiaeuk specific workflows

This PR may lead to different results in pre-existing outputs: No

This PR uses an element that could cause duplicate runs to have different results: No

🛠️ Changes

⚙️ Algorithm

• Included theiaeuk specific qc trimming happy path to wf_read_QC_trim_ont
• Adapted Snippy for variant calling with ONT data
• Included Candida Aruis ONT specific analyses in the Merlin Magic workflow

➡️ Inputs

The following inputs are mandatory for theiaeuk_ont

File read1
String samplename

The following inputs are optional for theiaeuk_ont

Int genome_length
String? assembler
String? assembler_options
Int dragonflye_cpu 
Int dragonflye_memory
Int dragonflye_disk_size
String medaka_model 
File gambit_db_genomes 
File gambit_db_signatures

⬅️ Outputs

# Version Capture
    String theiaeuk_ont_version = version_capture.phb_version
    String theiaeuk_ont_analysis_date = version_capture.date
    # Read QC outputs
    File read1_clean = read_qc.read1_clean
    String? nanoq_version = read_qc.nanoq_version
    Int est_genome_length = read_qc.est_genome_length
    # Assembly outputs
    File assembly_fasta = dragonflye.assembly_fasta
    File contigs_gfa = dragonflye.contigs_gfa
    String dragonflye_version = dragonflye.dragonflye_version
    # Read QC - nanoplot raw outputs
    File? nanoplot_html_raw = nanoplot_raw.nanoplot_html
    File? nanoplot_tsv_raw = nanoplot_raw.nanoplot_tsv
    Int? nanoplot_num_reads_raw1 = nanoplot_raw.num_reads
    Float? nanoplot_r1_median_readlength_raw = nanoplot_raw.median_readlength
    Float? nanoplot_r1_mean_readlength_raw = nanoplot_raw.mean_readlength
    Float? nanoplot_r1_stdev_readlength_raw = nanoplot_raw.stdev_readlength
    Float? nanoplot_r1_n50_raw = nanoplot_raw.n50
    Float? nanoplot_r1_mean_q_raw = nanoplot_raw.mean_q
    Float? nanoplot_r1_median_q_raw = nanoplot_raw.median_q
    Float? nanoplot_r1_est_coverage_raw = nanoplot_raw.est_coverage
    # Read QC - nanoplot clean outputs
    File? nanoplot_html_clean = nanoplot_clean.nanoplot_html
    File? nanoplot_tsv_clean = nanoplot_clean.nanoplot_tsv
    Int? nanoplot_num_reads_clean1 = nanoplot_clean.num_reads
    Float? nanoplot_r1_median_readlength_clean = nanoplot_clean.median_readlength
    Float? nanoplot_r1_mean_readlength_clean = nanoplot_clean.mean_readlength
    Float? nanoplot_r1_stdev_readlength_clean = nanoplot_clean.stdev_readlength
    Float? nanoplot_r1_n50_clean = nanoplot_clean.n50
    Float? nanoplot_r1_mean_q_clean = nanoplot_clean.mean_q
    Float? nanoplot_r1_median_q_clean = nanoplot_clean.median_q
    Float? nanoplot_r1_est_coverage_clean = nanoplot_clean.est_coverage
    # Read QC - nanoplot general outputs
    String? nanoplot_version = nanoplot_raw.nanoplot_version
    String? nanoplot_docker = nanoplot_raw.nanoplot_docker
    # Assembly QC - quast outputs
    File? quast_report = quast.quast_report
    String? quast_version = quast.version
    Int? assembly_length = quast.genome_length
    Int? number_contigs = quast.number_contigs
    Int? n50_value = quast.n50_value
    Float? quast_gc_percent = quast.gc_percent
    # Assembly QC - nanoplot outputs
    Float? est_coverage_raw = nanoplot_raw.est_coverage
    Float? est_coverage_clean = nanoplot_clean.est_coverage
    # Assembly QC - busco outputs
    String? busco_version = busco.busco_version
    String? busco_docker = busco.busco_docker
    String? busco_database = busco.busco_database
    String? busco_results = busco.busco_results
    File? busco_report = busco.busco_report
    # Gambit outputs
    File gambit_report_file = gambit.gambit_report_file
    File gambit_closest_genomes_file = gambit.gambit_closest_genomes_file
    String gambit_predicted_taxon = gambit.gambit_predicted_taxon
    String gambit_predicted_taxon_rank = gambit.gambit_predicted_taxon_rank
    String gambit_next_taxon = gambit.gambit_next_taxon
    String gambit_next_taxon_rank = gambit.gambit_next_taxon_rank
    String gambit_version = gambit.gambit_version
    String gambit_db_version = gambit.gambit_db_version
    String merlin_tag = gambit.merlin_tag
    String gambit_docker = gambit.gambit_docker
    # C. auris specific outputs for cladetyper
    String? clade_type = merlin_magic.clade_type
    String? cladetyper_analysis_date = merlin_magic.cladetyper_analysis_date
    String? cladetyper_version = merlin_magic.cladetyper_version
    String? cladetyper_docker_image = merlin_magic.cladetyper_docker_image
    String? cladetype_annotated_ref = merlin_magic.cladetype_annotated_ref
    # Snippy variants outputs
    String? snippy_variants_version = merlin_magic.snippy_variants_version
    String? snippy_variants_query = merlin_magic.snippy_variants_query
    String? snippy_variants_query_check = merlin_magic.snippy_variants_query_check
    String? snippy_variants_hits = merlin_magic.snippy_variants_hits
    String? snippy_variants_gene_query_results = merlin_magic.snippy_variants_gene_query_results
    String? snippy_variants_outdir_tarball = merlin_magic.snippy_variants_outdir_tarball
    String? snippy_variants_results = merlin_magic.snippy_variants_results
    String? snippy_variants_bam = merlin_magic.snippy_variants_bam
    String? snippy_variants_bai = merlin_magic.snippy_variants_bai
    String? snippy_variants_summary = merlin_magic.snippy_variants_summary
    String? snippy_variants_num_reads_aligned = merlin_magic.snippy_variants_num_reads_aligned
    String? snippy_variants_coverage_tsv = merlin_magic.snippy_variants_coverage_tsv
    String? snippy_variants_num_variants = merlin_magic.snippy_variants_num_variants
    String? snippy_variants_percent_ref_coverage = merlin_magic.snippy_variants_percent_ref_coverage

🧪 Testing

Suggested Scenarios for Reviewer to Test

🔬 Final Developer Checklist

• The workflow/task has been tested and results, including file contents, are as anticipated
• The CI/CD has been adjusted and tests are passing (Theiagen developers)
• Code changes follow the style guide
• Documentation and/or workflow diagrams have been updated if applicable (Theiagen developers only)

🎯 Reviewer Checklist

• All changed results have been confirmed
• You have tested the PR appropriately (see the testing guide for more information)
• All code adheres to the style guide
• MD5 sums have been updated
• The PR author has addressed all comments
• The documentation has been updated

[michellescribner]

I've launched some initial function tests here using ONT data from SRA for fungal pathogens and intend to explore how closely assembly lengths align with expected values.

Update: The samples tested all have either low coverage (<40X) or low mean base quality scores (<12). With that in mind, the de novo assemblies were often approximately the expected length for the species, but they showed many missing loci according to BUSCO (BUSCO completeness <60). High error rate is expected for these assemblies.

Higher quality/quantity read data may drastically improve the performance of TheiaEuk_ONT.