diff --git a/h5_structs.wdl b/h5_structs.wdl
new file mode 100644
index 0000000..184db69
--- /dev/null
+++ b/h5_structs.wdl
@@ -0,0 +1,100 @@
+version development-1.1
+
+struct Sample {
+    String name
+    String primer
+    File fastq1
+    File fastq2 
+    Int i
+}
+
+struct Reference {
+    String name
+    File fasta
+}
+
+struct PrimerScheme {
+    String name
+    Array[Reference] references
+    File bed
+}
+
+struct VersionInfo {
+  String software
+  String docker
+  String version
+}
+
+struct SampleReferenceOutputs {
+    String primer_scheme_name
+    String reference_name
+    Pair[String, File] bam
+    Pair[String, File] trimmed_sorted_bam
+    Pair[String, File] trimmed_sorted_bai
+    Pair[String, File] pileup
+    Pair[String, File] consensus_fasta
+    Pair[String, File] samtools_coverage
+    Pair[String, File] samtools_stats
+    Pair[String, File] coverage_stats
+}
+
+workflow declare_structs {
+    input {
+        File bovine_texas_029328_01_UtoT_ha_fasta
+        File bovine_texas_029328_01_UtoT_fasta
+        File darwin_9_2021_h3n2_ha_h3_fasta
+        File victoria_4897_2022_h1n1_ha_h1_fasta
+        File vietnam_1203_2024_h5n1_ha_v2_fasta  
+        File human_h5_250_bed
+        File houston_bed
+        File AVRL_H5N1_250bp_bed
+    }
+    Reference vietnam_1203_2024_h5n1_ha_v2 = Reference {
+        name: "vietnam_1203_2024_h5n1_ha_v2",
+        fasta: vietnam_1203_2024_h5n1_ha_v2_fasta
+    }
+    Reference bovine_texas_029328_01_UtoT_ha = Reference {
+        name: "bovine_texas_029328_01_UtoT_ha",
+        fasta: bovine_texas_029328_01_UtoT_ha_fasta
+    }
+    Reference bovine_texas_029328_01_UtoT = Reference {
+        name: "bovine_texas_029328_01_UtoT",
+        fasta: bovine_texas_029328_01_UtoT_fasta
+    }
+    Reference darwin_9_2021_h3n2_ha_h3 = Reference {
+        name: "darwin_9_2021_h3n2_ha_h3",
+        fasta: darwin_9_2021_h3n2_ha_h3_fasta
+    }
+    Reference victoria_4897_2022_h1n1_ha_h1 = Reference {
+        name: "victoria_4897_2022_h1n1_ha_h1",
+        fasta: victoria_4897_2022_h1n1_ha_h1_fasta
+    }
+
+    PrimerScheme human_h5_250 = PrimerScheme {
+        name: "human_h5_250",
+        references:   [vietnam_1203_2024_h5n1_ha_v2, 
+                            bovine_texas_029328_01_UtoT_ha],
+        bed: human_h5_250_bed
+    }
+    PrimerScheme houston = PrimerScheme {
+        name: "houston",
+        references:  [darwin_9_2021_h3n2_ha_h3, 
+                            victoria_4897_2022_h1n1_ha_h1, 
+                            bovine_texas_029328_01_UtoT_ha],
+        bed: houston_bed
+    }
+    PrimerScheme AVRL_H5N1_250bp = PrimerScheme {
+        name: "AVRL_H5N1_250bp",
+        references: [bovine_texas_029328_01_UtoT],
+        bed: AVRL_H5N1_250bp_bed
+    }
+
+    output {
+        Array[PrimerScheme] primer_schemes = [human_h5_250, houston, AVRL_H5N1_250bp] 
+        Array[Reference] references = [vietnam_1203_2024_h5n1_ha_v2, 
+                                        bovine_texas_029328_01_UtoT_ha, 
+                                        darwin_9_2021_h3n2_ha_h3, 
+                                        victoria_4897_2022_h1n1_ha_h1,
+                                        bovine_texas_029328_01_UtoT]
+    }
+}
\ No newline at end of file
diff --git a/h5_testing.wdl b/h5_testing.wdl
new file mode 100644
index 0000000..f25621b
--- /dev/null
+++ b/h5_testing.wdl
@@ -0,0 +1,523 @@
+version development-1.1
+
+import "h5_structs.wdl" as sub
+
+workflow h5 {
+    input {
+        Array[String] primers
+        Array[String] samples
+        Array[File] fastq1s
+        Array[File] fastq2s
+        String project_name
+        String gs_dir = 'gs://arianna_sandbox/h5'
+        File contaminants_fasta
+        File human_h5_250_bed
+        File houston_bed
+        File AVRL_H5N1_250bp_bed
+
+        # All of these reference fastas are HA gene segments
+        File bovine_texas_029328_01_UtoT_ha_fasta
+        File darwin_9_2021_h3n2_ha_h3_fasta
+        File victoria_4897_2022_h1n1_ha_h1_fasta
+        File vietnam_1203_2024_h5n1_ha_v2_fasta    
+    
+        # Whole genome references
+        File bovine_texas_029328_01_UtoT_fasta
+    }
+
+    # private declarations
+    String fastqc_docker = 'staphb/fastqc:0.12.1'
+    String seqyclean_docker = 'staphb/seqyclean:1.10.09'
+    String bwa_docker = 'staphb/bwa:0.7.17'
+    String samtools_docker = 'staphb/samtools:1.10'
+    String ivar_docker = 'staphb/ivar:1.4.2'
+    String python_docker = 'ariannaesmith/py3.10.9-bio'
+    String viral_core_docker = 'quay.io/broadinstitute/viral-core:2.2.3'
+    String multiqc_docker = 'staphb/multiqc:1.8'
+    String jammy_docker = 'ubuntu:jammy-20240627.1'
+    String utility_docker = 'theiagen/utility:1.0'
+
+    Array[Int] indexes = range(length(samples))
+
+    String project_outdir = gs_dir + "/" +  project_name + "/"
+
+    # Struct initilizations
+    call sub.declare_structs as s {
+        input: 
+            bovine_texas_029328_01_UtoT_ha_fasta = bovine_texas_029328_01_UtoT_ha_fasta,
+            darwin_9_2021_h3n2_ha_h3_fasta = darwin_9_2021_h3n2_ha_h3_fasta,
+            victoria_4897_2022_h1n1_ha_h1_fasta = victoria_4897_2022_h1n1_ha_h1_fasta,
+            vietnam_1203_2024_h5n1_ha_v2_fasta = vietnam_1203_2024_h5n1_ha_v2_fasta,
+            bovine_texas_029328_01_UtoT_fasta = bovine_texas_029328_01_UtoT_fasta,
+            human_h5_250_bed = human_h5_250_bed,
+            houston_bed = houston_bed,
+            AVRL_H5N1_250bp_bed = AVRL_H5N1_250bp_bed
+    }
+
+    # Scatter samples to create structs
+    scatter (idx in indexes) {
+        Sample sample = Sample {
+            name: samples[idx],
+            primer: primers[idx],
+            fastq1: fastq1s[idx],
+            fastq2: fastq2s[idx],
+            i: idx
+        }
+    }
+
+    Array[Sample] all_samples = sample
+    # Group samples by primer
+    scatter (ps in s.primer_schemes) {
+        
+        scatter (samp in all_samples) {
+            if (samp.primer == ps.name) {
+                Sample primer_sample = samp
+                Int match_index = samp.i
+            }
+        }
+
+        Boolean primer_sample_matches = defined(primer_sample)
+        if (primer_sample_matches) {
+            # This first line is only included because the following fails without it?
+            Array[Int] index_matches = select_all(match_index)
+            Array[Sample] primer_samples = select_all(primer_sample)
+        }        
+        # if !(primer_sample_matches) {
+        #     call exit_wdl {input: exit_reason = "primer not used"}
+        # }
+
+        String primer_outdir = project_outdir + ps.name +"/"
+        # Call primer level tasks
+        scatter (samp in primer_samples) {
+            # Call sample level tasks
+            call fastqc as fastqc_raw {
+                input: 
+                    sample = samp, 
+                    fastq1 = samp.fastq1, 
+                    fastq2 = samp.fastq2, 
+                    docker = fastqc_docker
+            }
+
+            # call sample_qc_file as sample_qc_file_raw {
+            #     input: 
+            #         sample_name = samp.name,
+            #         fastqc1_data = fastqc_raw.fastqc1_data,
+            #         fastqc2_data = fastqc_raw.fastqc2_data,
+            #         docker = python_docker
+            # }
+            
+            call seqyclean {
+                input: 
+                    sample = samp,
+                    contaminants_fasta = contaminants_fasta,
+                    docker = seqyclean_docker
+            }
+
+            call fastqc as fastqc_clean {
+                input: 
+                    sample = samp, 
+                    fastq1 = seqyclean.PE1, 
+                    fastq2 = seqyclean.PE2, 
+                    docker = fastqc_docker
+            }
+
+            # call sample_qc_file as sample_qc_file_clean {
+            #     input: 
+            #         sample_name = samp.name,
+            #         fastqc1_data = fastqc_clean.fastqc1_data,
+            #         fastqc2_data = fastqc_clean.fastqc2_data,
+            #         docker = python_docker
+            # }
+        }
+
+        Array[String] task_dirs = ["fastqc_raw", "fastqc_clean", "seqyclean"]
+        Array[Array[File]] task_files = [flatten([fastqc_raw.fastqc1_data, fastqc_raw.fastqc2_data, sample_qc_file_raw.summary_metrics]),
+                            flatten([fastqc_clean.fastqc1_data, fastqc_clean.fastqc2_data, sample_qc_file_clean.summary_metrics]),
+                            flatten([seqyclean.PE1, seqyclean.PE2])]
+    
+        call transfer as transfer_primer_tasks {
+            input:
+                out_dir = primer_outdir,
+                task_dirs = task_dirs,
+                task_files = task_files,
+                docker = utility_docker
+        }
+        
+    }
+
+
+}
+
+task transfer {
+    input {
+        String out_dir
+        Array[String] task_dirs
+        Array[Array[File]] task_files
+        String docker
+    }
+
+    Array[Int] indexes = range(length(task_dirs))
+
+    command <<<
+        for i in "${!indexes[@]}"; do gsutil -m cp "${task_files[$i]} ~{out_dir}${task_dirs[$i]}/"; done;
+    >>>
+    runtime {
+        #cpu: ,
+        #memory: ,
+        docker: docker
+    }
+}
+
+task multiqc {
+    input {
+        Array[File] fastq1s
+        Array[File] fastq2s
+        String fastq_type
+        String docker
+    }
+    String fastq_dir = "~{fastq_type}_fastqs/"
+    String out_dir = "multiqc_~{fastq_type}/"
+
+    command <<<
+        mkdir ~{fastq_dir}
+        cp ~{sep(' ', fastq1s)} ~{fastq_dir}
+        cp ~{sep(' ', fastq2s)} ~{fastq_dir}
+        multiqc ~{fastq_dir} --outdir
+    >>>
+
+    output {
+        Array[File] fastqs_dir = glob("~{out_dir}*")
+    }
+    runtime {
+        #cpu: ,
+        #memory: ,
+        maxRetries: 0,
+        docker: docker
+    }
+}
+
+task fastqc {
+    input {
+        Sample sample
+        File fastq1
+        File fastq2
+        String docker
+    }
+
+        String fastq1_name = basename(fastq1, ".fastq.gz")
+        String fastq2_name = basename(fastq2, ".fastq.gz")
+
+    command <<<
+        fastqc --extract --delete ~{sample.fastq1} ~{sample.fastq2}
+        cp "_miniwdl_inputs/0/~{fastq1_name}_fastqc/fastqc_data.txt" "~{fastq1_name}_fastqc_data.txt"
+        cp "_miniwdl_inputs/0/~{fastq2_name}_fastqc/fastqc_data.txt" "~{fastq2_name}_fastqc_data.txt"
+        fastqc --version | awk '/FastQC/ {print $2}' | tee VERSION    
+        >>>
+
+    output {
+        File fastqc1_data = "~{fastq1_name}_fastqc_data.txt"
+        File fastqc2_data = "~{fastq2_name}_fastqc_data.txt"
+        String version = read_string('VERSION')
+    }
+
+    runtime {
+        #cpu: ,
+        #memory: ,
+        maxRetries: 0,
+        docker: docker
+    }
+}
+
+task sample_qc_file {
+    input {
+        String sample_name
+        File fastqc1_data
+        File fastqc2_data
+        String docker
+    }
+
+    command <<<
+        # python things
+    >>>
+
+    output {
+        File summary_metrics = "${sample_name}_summary_metrics.tsv"
+    }
+
+    runtime {
+        #cpu: ,
+        #memory: ,
+        docker: docker
+    }
+}
+
+task seqyclean {
+    input {
+        Sample sample
+        File contaminants_fasta
+        String docker
+    }
+
+    String out_name = "seqyclean/~{sample.name}_clean"
+
+    command <<<
+        seqyclean -minlen 25 -qual 30 30 -gz -1 ~{sample.fastq1} -2 ~{sample.fastq2} -c ~{contaminants_fasta} -o ~{out_name}
+    >>>
+
+    output {
+        File PE1 = "seqyclean/~{sample.name}_clean_PE1.fastq.gz"
+        File PE2 = "seqyclean/~{sample.name}_clean_PE2.fastq.gz"
+    }
+
+    runtime {
+        #cpu: ,
+        #memory: ,
+        docker: docker
+    }
+}
+
+task align_bwa {
+    input {
+        String sample_name
+        File fastq1
+        File fastq2
+        String reference_name
+        File reference_fasta
+        String docker
+    }
+
+    String sam_fn = sample_name + ".sam"
+    String bam_fn = sample_name + "aln.sorted.bam"
+
+    command <<<
+        bwa index -p ~{reference_name} -a is ~{reference_fasta}
+        bwa mem -t 6 ~{reference_name} ~{fastq1} ~{fastq2} -f ~{sam_fn}
+        samtools view -bS ~{sam_fn} | samtools sort -o {bam_fn}
+    >>>
+
+    output {
+        File bam = bam_fn
+    }
+
+    runtime {
+        #cpu: ,
+        #memory: ,
+        docker: docker
+    }
+}
+
+task trim_primers_ivar {
+    input {
+        String sample_name
+        File bam
+        File primer_bed
+        String docker
+    }
+
+    String trim_fn = sample_name + "_trimmed.bam"
+    String trim_sort_bam_fn = sample_name + "_trimmed.sorted.bam"
+    String trim_sort_bai_fn = sample_name + "_trimmed.sorted.bai"
+    
+    command <<<
+        ivar trim -e -i ~{bam} -b ~{primer_bed} -p ~{trim_fn}
+        samtools sort ~{trim_fn} -o ~{trim_sort_bam_fn}
+        samtools index ~{trim_sort_bam_fn}
+    >>>
+
+    output {
+        File trimmed_sorted_bam = trim_sort_bam_fn
+        File trimmed_sorted_bai = trim_sort_bai_fn
+    }
+
+    runtime {
+        #cpu: ,
+        #memory: ,
+        docker: docker
+    }
+}
+
+task generate_consensus_ivar {
+    input {
+        String sample_name
+        File trimmed_sorted_bam
+        File reference_fasta
+       String docker
+    }
+
+    String pileup_fn = sample_name + "_pileup.txt"
+    String consensus_fn_prefix = sample_name + "_consensus"
+
+    command <<<
+        samtools faidx ~{reference_fasta}
+        samtools mpileup -A -aa -d 600000 -B -Q 20 -q 20 -f ~{reference_fasta} ~{trimmed_sorted_bam} -o ~{pileup_fn}
+        cat ~{pileup_fn} | ivar consensus -p ~{consensus_fn_prefix} -q 20 -t 0.6 -m 10
+    >>>
+
+    output {
+        File pileup = pileup_fn
+        File consensus_fasta = consensus_fn_prefix + ".fa"
+    }
+
+    runtime {
+        #cpu: ,
+        #memory: ,
+        docker: docker
+    }
+}
+
+task alignment_metrics {
+    input {
+        String sample_name
+        File trimmed_sorted_bam
+        File reference_fasta
+        String docker
+    }
+
+    String coverage_fn = sample_name + "_coverage.txt"
+    String stats_fn = sample_name + "_stats.txt"
+
+    command <<<
+        samtools coverage -o ~{coverage_fn} ~{trimmed_sorted_bam}
+        samtools stats ~{trimmed_sorted_bam} > ~{stats_fn}
+    >>>
+
+    output {
+        File coverage = coverage_fn
+        File stats = stats_fn
+    }
+
+    runtime {
+        #cpu: ,
+        #memory: ,
+        docker: docker
+    }
+}
+
+task calculate_coverage_stats {
+    input {
+        Int ref_length
+        Int seq_ref_length
+        String sample_name
+        File consensus_fasta
+        String docker
+    }
+
+    command <<<
+        # python stuff
+    >>>
+
+    output {
+        File coverage_stats = "~{sample_name}_coverage_stats.csv"
+    }
+
+    runtime {
+        #cpu: ,
+        #memory: ,
+        docker: docker
+    }
+}
+
+task concat_sample_reference_metrics {
+    input {
+        String sample_name
+        File samtools_coverage
+        File samtools_stats
+        File coverage_stats
+        String docker
+    }
+
+    command <<<
+        # python things
+    >>>
+
+    output {
+        File sample_reference_metrics = "~{sample_name}_reference_metrics.csv"
+    }
+
+    runtime {
+        #cpu: ,
+        #memory: ,
+        docker: docker
+    }
+}
+
+task concat_sample_metrics {
+    input {
+        String sample_name
+        Array[File] sample_reference_metrics
+        String docker
+    }
+
+    command <<<
+        # python things
+    >>>
+
+    output {
+        File sample_metrics = "~{sample_name}_metrics.csv"
+    }
+
+    runtime {
+        #cpu: ,
+        #memory: ,
+        docker: docker
+    }
+}
+
+task concat_all_samples_metrics {
+    input {
+        Array[File] sample_metrics_files
+        String docker
+    }
+
+    command <<<
+        # python things
+    >>>
+
+    output {
+        File samples_metrics = "summary_metrics.csv"
+    }
+
+    runtime {
+        #cpu: ,
+        #memory: ,
+        docker: docker
+    }
+}
+
+
+
+task echo_things {
+    input {
+        String out_dir
+        String sample_name
+        String sample_primer_scheme
+        PrimerScheme? primer_scheme
+        String fastq1
+        String fastq2
+        }
+
+    command <<<
+        echo ~{out_dir}
+        echo ~{sample_name}
+        echo "~{sample_primer_scheme} should match ~{primer_scheme.name}"
+        echo ~{fastq1}
+        echo ~{fastq2}
+    >>>
+
+}
+
+task exit_wdl {
+    input {
+        String exit_reason
+    }
+    
+    command <<<
+        echo "~{exit_reason}"
+        exit 1
+    >>>
+
+    runtime {
+        returnCodes: 0
+        docker: "ubuntu:latest"
+    }
+}
\ No newline at end of file