# simulate_illumina_reads
Generate synthetic Illumina read sets for testing using wgsim. Takes a space-separated string of colon-separated pairs where each pair consists of a GenBank accession and a coverage value (e.g., 'KJ660346.2:12.5x NC_004296.1:0.9X'), downloads the sequences, and simulates Illumina reads.

## Inputs

### Required inputs
<p name="simulate_illumina_reads.accession_coverage_string">
        <b>simulate_illumina_reads.accession_coverage_string</b><br />
        <i>String &mdash; Default: None</i><br />
        Space-separated string of colon-separated pairs where each pair consists of a GenBank accession and a coverage value (e.g., 'KJ660346.2:12.5x NC_004296.1:0.9X').
</p>
<p name="simulate_illumina_reads.download_fasta_from_accession_string.emailAddress">
        <b>simulate_illumina_reads.download_fasta_from_accession_string.emailAddress</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>

### Other common inputs
<p name="simulate_illumina_reads.out_basename">
        <b>simulate_illumina_reads.out_basename</b><br />
        <i>String &mdash; Default: "simulated_reads"</i><br />
        Base name for output files.
</p>

### Advanced inputs
<details>
<summary> Show/Hide </summary>
<p name="simulate_illumina_reads.simulate_reads.coverage_bed">
        <b>simulate_illumina_reads.simulate_reads.coverage_bed</b><br />
        <i>File? &mdash; Default: None</i><br />
        Optional BED file specifying coverage per region. If provided, this overrides coverage_string.
</p>
<p name="simulate_illumina_reads.simulate_reads.indel_extend_probability">
        <b>simulate_illumina_reads.simulate_reads.indel_extend_probability</b><br />
        <i>Float? &mdash; Default: None</i><br />
        Probability an indel is extended (default: 0.3).
</p>
<p name="simulate_illumina_reads.simulate_reads.indel_fraction">
        <b>simulate_illumina_reads.simulate_reads.indel_fraction</b><br />
        <i>Float? &mdash; Default: None</i><br />
        Fraction of mutations that are indels (default: 0.15).
</p>
<p name="simulate_illumina_reads.simulate_reads.mutation_rate">
        <b>simulate_illumina_reads.simulate_reads.mutation_rate</b><br />
        <i>Float? &mdash; Default: None</i><br />
        Base mutation rate (default: 0.001).
</p>
<p name="simulate_illumina_reads.simulate_reads.outer_distance">
        <b>simulate_illumina_reads.simulate_reads.outer_distance</b><br />
        <i>Int? &mdash; Default: None</i><br />
        Outer distance between paired reads (default: 500bp).
</p>
<p name="simulate_illumina_reads.simulate_reads.random_seed">
        <b>simulate_illumina_reads.simulate_reads.random_seed</b><br />
        <i>Int? &mdash; Default: None</i><br />
        Random seed for reproducibility.
</p>
<p name="simulate_illumina_reads.simulate_reads.read_length">
        <b>simulate_illumina_reads.simulate_reads.read_length</b><br />
        <i>Int? &mdash; Default: None</i><br />
        Length of simulated reads (default: 150bp).
</p>
</details>

### Other inputs
<details>
<summary> Show/Hide </summary>
<p name="simulate_illumina_reads.download_fasta_from_accession_string.docker">
        <b>simulate_illumina_reads.download_fasta_from_accession_string.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-phylo"</i><br />
        ???
</p>
<p name="simulate_illumina_reads.simulate_reads.docker">
        <b>simulate_illumina_reads.simulate_reads.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-assemble"</i><br />
        ???
</p>
<p name="simulate_illumina_reads.simulate_reads.machine_mem_gb">
        <b>simulate_illumina_reads.simulate_reads.machine_mem_gb</b><br />
        <i>Int &mdash; Default: 7</i><br />
        ???
</p>
</details>

## Outputs
<p name="simulate_illumina_reads.read_count">
        <b>simulate_illumina_reads.read_count</b><br />
        <i>Int</i><br />
        ???
</p>
<p name="simulate_illumina_reads.reference_sequences">
        <b>simulate_illumina_reads.reference_sequences</b><br />
        <i>File</i><br />
        ???
</p>
<p name="simulate_illumina_reads.simulated_reads_bam">
        <b>simulate_illumina_reads.simulated_reads_bam</b><br />
        <i>File</i><br />
        ???
</p>
<p name="simulate_illumina_reads.viralngs_version">
        <b>simulate_illumina_reads.viralngs_version</b><br />
        <i>String</i><br />
        ???
</p>

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> Generated using WDL AID (1.0.0)