# load_illumina_fastqs
Process DRAGEN FASTQ files into per-sample BAM files with demultiplexing support.

## Inputs

### Required inputs
<p name="load_illumina_fastqs.fastq_files">
        <b>load_illumina_fastqs.fastq_files</b><br />
        <i>Array[File] &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs.runinfo_xml">
        <b>load_illumina_fastqs.runinfo_xml</b><br />
        <i>File &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs.samplesheet">
        <b>load_illumina_fastqs.samplesheet</b><br />
        <i>File &mdash; Default: None</i><br />
        ???
</p>

### Advanced inputs
<details>
<summary> Show/Hide </summary>
<p name="load_illumina_fastqs.demux_fastqs.run_fastqc">
        <b>load_illumina_fastqs.demux_fastqs.run_fastqc</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        Whether to run FastQC on output BAM files. Set to false to skip FastQC and return empty arrays for fastqc_html and fastqc_zip outputs.
</p>
<p name="load_illumina_fastqs.get_illumina_run_metadata.lane">
        <b>load_illumina_fastqs.get_illumina_run_metadata.lane</b><br />
        <i>Int? &mdash; Default: None</i><br />
        Lane number. Optional - if not specified, illumina.py will use all lanes or default behavior.
</p>
<p name="load_illumina_fastqs.get_illumina_run_metadata.sequencing_center">
        <b>load_illumina_fastqs.get_illumina_run_metadata.sequencing_center</b><br />
        <i>String? &mdash; Default: None</i><br />
        Sequencing center name (default: Broad).
</p>
</details>

### Other inputs
<details>
<summary> Show/Hide </summary>
<p name="load_illumina_fastqs.check_for_barcode3.docker">
        <b>load_illumina_fastqs.check_for_barcode3.docker</b><br />
        <i>String &mdash; Default: "python:slim"</i><br />
        ???
</p>
<p name="load_illumina_fastqs.demux_cpu_no_splitcode">
        <b>load_illumina_fastqs.demux_cpu_no_splitcode</b><br />
        <i>Int &mdash; Default: 4</i><br />
        ???
</p>
<p name="load_illumina_fastqs.demux_cpu_splitcode">
        <b>load_illumina_fastqs.demux_cpu_splitcode</b><br />
        <i>Int &mdash; Default: 32</i><br />
        ???
</p>
<p name="load_illumina_fastqs.demux_fastqs.disk_size">
        <b>load_illumina_fastqs.demux_fastqs.disk_size</b><br />
        <i>Int &mdash; Default: 750</i><br />
        ???
</p>
<p name="load_illumina_fastqs.demux_fastqs.docker">
        <b>load_illumina_fastqs.demux_fastqs.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-core:2.5.10"</i><br />
        ???
</p>
<p name="load_illumina_fastqs.demux_fastqs.machine_mem_gb">
        <b>load_illumina_fastqs.demux_fastqs.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs.demux_fastqs.sequencingCenter">
        <b>load_illumina_fastqs.demux_fastqs.sequencingCenter</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs.demux_memory_no_splitcode">
        <b>load_illumina_fastqs.demux_memory_no_splitcode</b><br />
        <i>Int &mdash; Default: 15</i><br />
        ???
</p>
<p name="load_illumina_fastqs.demux_memory_splitcode">
        <b>load_illumina_fastqs.demux_memory_splitcode</b><br />
        <i>Int &mdash; Default: 120</i><br />
        ???
</p>
<p name="load_illumina_fastqs.get_illumina_run_metadata.docker">
        <b>load_illumina_fastqs.get_illumina_run_metadata.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-core:2.5.10"</i><br />
        ???
</p>
<p name="load_illumina_fastqs.get_illumina_run_metadata.machine_mem_gb">
        <b>load_illumina_fastqs.get_illumina_run_metadata.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs.merge_demux_metrics.docker">
        <b>load_illumina_fastqs.merge_demux_metrics.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-core:2.5.10"</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.comment">
        <b>load_illumina_fastqs.MultiQC.comment</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.config">
        <b>load_illumina_fastqs.MultiQC.config</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.config_yaml">
        <b>load_illumina_fastqs.MultiQC.config_yaml</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.data_dir">
        <b>load_illumina_fastqs.MultiQC.data_dir</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.docker">
        <b>load_illumina_fastqs.MultiQC.docker</b><br />
        <i>String &mdash; Default: "quay.io/biocontainers/multiqc:1.32--pyhdfd78af_1"</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.exclude_modules">
        <b>load_illumina_fastqs.MultiQC.exclude_modules</b><br />
        <i>Array[String]? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.export">
        <b>load_illumina_fastqs.MultiQC.export</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.file_name">
        <b>load_illumina_fastqs.MultiQC.file_name</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.flat">
        <b>load_illumina_fastqs.MultiQC.flat</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.force">
        <b>load_illumina_fastqs.MultiQC.force</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.full_names">
        <b>load_illumina_fastqs.MultiQC.full_names</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.ignore_analysis_files">
        <b>load_illumina_fastqs.MultiQC.ignore_analysis_files</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.ignore_sample_names">
        <b>load_illumina_fastqs.MultiQC.ignore_sample_names</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.interactive">
        <b>load_illumina_fastqs.MultiQC.interactive</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.lint">
        <b>load_illumina_fastqs.MultiQC.lint</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.megaQC_upload">
        <b>load_illumina_fastqs.MultiQC.megaQC_upload</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.module_to_use">
        <b>load_illumina_fastqs.MultiQC.module_to_use</b><br />
        <i>Array[String]? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.no_data_dir">
        <b>load_illumina_fastqs.MultiQC.no_data_dir</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.out_dir">
        <b>load_illumina_fastqs.MultiQC.out_dir</b><br />
        <i>String &mdash; Default: "./multiqc-output"</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.output_data_format">
        <b>load_illumina_fastqs.MultiQC.output_data_format</b><br />
        <i>String? &mdash; Default: None</i><br />
        [tsv|yaml|json] default:tsv
</p>
<p name="load_illumina_fastqs.MultiQC.pdf">
        <b>load_illumina_fastqs.MultiQC.pdf</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.sample_names">
        <b>load_illumina_fastqs.MultiQC.sample_names</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.tag">
        <b>load_illumina_fastqs.MultiQC.tag</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.template">
        <b>load_illumina_fastqs.MultiQC.template</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.title">
        <b>load_illumina_fastqs.MultiQC.title</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs.MultiQC.zip_data_dir">
        <b>load_illumina_fastqs.MultiQC.zip_data_dir</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
</details>

## Outputs
<p name="load_illumina_fastqs.demux_metrics">
        <b>load_illumina_fastqs.demux_metrics</b><br />
        <i>File</i><br />
        ???
</p>
<p name="load_illumina_fastqs.fastqc_html">
        <b>load_illumina_fastqs.fastqc_html</b><br />
        <i>Array[File]</i><br />
        ???
</p>
<p name="load_illumina_fastqs.fastqc_zip">
        <b>load_illumina_fastqs.fastqc_zip</b><br />
        <i>Array[File]</i><br />
        ???
</p>
<p name="load_illumina_fastqs.meta_by_filename">
        <b>load_illumina_fastqs.meta_by_filename</b><br />
        <i>Map[String,Map[String,String]]</i><br />
        ???
</p>
<p name="load_illumina_fastqs.meta_by_filename_json">
        <b>load_illumina_fastqs.meta_by_filename_json</b><br />
        <i>File</i><br />
        ???
</p>
<p name="load_illumina_fastqs.meta_by_sample">
        <b>load_illumina_fastqs.meta_by_sample</b><br />
        <i>Map[String,Map[String,String]]</i><br />
        ???
</p>
<p name="load_illumina_fastqs.meta_by_sample_json">
        <b>load_illumina_fastqs.meta_by_sample_json</b><br />
        <i>File</i><br />
        ???
</p>
<p name="load_illumina_fastqs.multiqc_data_tar_gz">
        <b>load_illumina_fastqs.multiqc_data_tar_gz</b><br />
        <i>File</i><br />
        ???
</p>
<p name="load_illumina_fastqs.multiqc_report">
        <b>load_illumina_fastqs.multiqc_report</b><br />
        <i>File</i><br />
        ???
</p>
<p name="load_illumina_fastqs.raw_reads_unaligned_bams">
        <b>load_illumina_fastqs.raw_reads_unaligned_bams</b><br />
        <i>Array[File]</i><br />
        ???
</p>
<p name="load_illumina_fastqs.read_counts_raw">
        <b>load_illumina_fastqs.read_counts_raw</b><br />
        <i>Array[Int]</i><br />
        ???
</p>
<p name="load_illumina_fastqs.run_info">
        <b>load_illumina_fastqs.run_info</b><br />
        <i>Map[String,String]</i><br />
        ???
</p>
<p name="load_illumina_fastqs.run_info_json">
        <b>load_illumina_fastqs.run_info_json</b><br />
        <i>File</i><br />
        ???
</p>
<p name="load_illumina_fastqs.viralngs_version">
        <b>load_illumina_fastqs.viralngs_version</b><br />
        <i>String</i><br />
        ???
</p>

<hr />

> Generated using WDL AID (1.0.0)