README.md

DISCLAIMER

This repository is in active development and is not yet ready for production use.

CDPHE-H5-Influenza workflow

Disclaimer

Next generation sequencing and bioinformatic and genomic analysis at the Colorado Department of Public Health and Environment (CDPHE) is not CLIA validated at this time. These workflows and their outputs are not to be used for diagnostic purposes and should only be used for public health action and surveillance purposes. CDPHE is not responsible for the incorrect or inappropriate use of these workflows or their results.

Overview

The following documentation describes the Colorado Department of Public Health and Environment's workflows for the assembly and analysis of next genome sequencing data of H5 influenza on GCP's Terra.bio platform.

The workflow currently allows for various primer schemes and references for alignment. Some are only for the HA gene segment while others are whole genome. See Workspace data below.

The workflow is split into multiple wdl files, but is all launched as one workflow.

Files

Subworkflows

Name	Description	Subworkflow/task calls
h5_testing	The main workflow that calls all other subworkflows and tasks.	version_capture_tasks.workflow_metadata h5_structs.declare_structs primer_tasks.primer_level_tasks reference_tasks.reference_level_tasks version_capture_tasks.capture_versions other_tasks.transfer_vc
h5_structs	Contains struct definitions and subworkflow to declare the primer schemes and references structs.	None
primer_tasks	Subworkflow and task declarations for primer-level tasks.	fastqc_raw seqyclean fastqc_clean sample_qc_file multiqc_fastqc multiqc_seqyclean transfer
reference_tasks	Subworkflow and task declarations for reference-level tasks.	align_bwa trim_primers_ivar generate_consensus_ivar alignment_metrics calculate_percent_coverage concat_sample_reference_metrics multiqc_samtools transfer
version_capture_tasks	Task declarations for tool and workflow version capture.	workflow_metadata capture_versions
other_tasks	Task declarations for all other tasks.	transfer multiqc concat_all_samples_metrics

Flow

Note- Commonly-used inputs such as sample_name are not noted below.

• Call version_capture_tasks.workflow_metadata task to get the workflow version and analysis date.
• Call h5_structs.declare_structs subworkflow to declare reference and primer scheme struct objects.
• Scatter samples to create Sample struct objects.
• Scatter PrimerScheme array.
  • Create primer sample list, excluding those with empty fastq files.
  • Call primer_tasks.primer_level_tasks subworkflow
    • Scatter samples
      • Call fastqc_raw. Input - raw fastq files.
      • Call seqyclean. Input - raw fastq files.
      • Call fastqc_clean. Input - cleaned fastq files from seqyclean.
    • Call sample_qc_file. Input - data.txt files from fastqc_raw and fastqc_clean, SummaryStatistics.txt from seqyclean.
    • Call multiqc_fastqc. Input- data.txt files from fastqc_raw and fastqc_clean.
    • Call multiqc_seqyclean. Input- SummaryStatistics.txt files from seqyclean.
    • Call other_tasks.transfer task to transfer all primer-level task outputs to their respective directories.
  • Call reference_tasks.reference_level_tasks subworkflow
    • Scatter samples
      • Call align_bwa. Input - reference name and fasta file, cleaned fastq files from seqyclean.
      • Call trim_primers_ivar. Input - bwa from align_bwa, primer_bed file
      • Call generate_consensus_ivar. Input - trimmed.sorted.bam from trim_primers_ivar, reference fasta file.
      • Call alignment_metrics. Input - trimmed.sorted.bam from trim_primers_ivar
      • Call calculate_percent_coverage. Input - {to fill in}
      • Call concat_sample_reference_metrics. Input - stats.txt and coverage.txt from alignment_metrics, coverage_stats.csv from calculate_percent_coverage.
    • Call multiqc_samtools. Input - stats.txt and coverage.txt from alignment_metrics.
    • Call other_tasks.transfer task to transfer all reference-level task outputs to their respective directories.
• Call version_capture_tasks.capture_versions. Input:analysis_date and workflow_version from workflow_metadata, Array[VersionInfo] objects from all tools used.
• Call other_tasks.transfer task to transfer version_capture.csv from version_capture_tasks.capture_versions.

Workspace data

Name	Description
AVRL_H5N1_250bp_bed	cattle-specific, tiled whole genome
houston_bed	Rice, H1, H3, H5, N1, N2 - Olivar (tiled)
human_h5_200_bed	cattle-H5-specific, 200bp, tiled HA gene
human_h5_250_bed	cattle-H5-specific, 250bp, tiled HA gene
bovine_texas_029328_01_UtoT_fasta	Cattle reference, whole genome
bovine_texas_029328_01_UtoT_ha_fasta	Cattle reference, HA gene
darwin_9_2021_h3n2_ha_h3_fasta	CDC vaccine strain reference for H3N2, HA gene
victoria_4897_2022_h1n1_ha_h1_fasta	CDC vaccine strain reference for H1N1, HA gene
vietnam_1203_2024_h5n1_ha_v2_fasta	CDC vaccine strain reference for H5N1, HA gene
contaminants_fasta	Adapters and contaminants fasta file