# 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.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: derived from RunInfo.xml).
</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_fastqs.cpu">
        <b>load_illumina_fastqs.demux_fastqs.cpu</b><br />
        <i>Int? &mdash; Default: None</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: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</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_max_cpu_no_splitcode">
        <b>load_illumina_fastqs.demux_max_cpu_no_splitcode</b><br />
        <i>Int &mdash; Default: 16</i><br />
        ???
</p>
<p name="load_illumina_fastqs.demux_max_cpu_splitcode">
        <b>load_illumina_fastqs.demux_max_cpu_splitcode</b><br />
        <i>Int &mdash; Default: 64</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: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</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: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="load_illumina_fastqs.merge_sample_metadata.out_meta_by_filename">
        <b>load_illumina_fastqs.merge_sample_metadata.out_meta_by_filename</b><br />
        <i>String &mdash; Default: "merged_meta_by_filename.json"</i><br />
        ???
</p>
<p name="load_illumina_fastqs.merge_sample_metadata.out_meta_by_sample">
        <b>load_illumina_fastqs.merge_sample_metadata.out_meta_by_sample</b><br />
        <i>String &mdash; Default: "merged_meta_by_sample.json"</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.cpu">
        <b>load_illumina_fastqs.multiqc.cpu</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs.multiqc.disk_size_gb">
        <b>load_illumina_fastqs.multiqc.disk_size_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs.multiqc.docker">
        <b>load_illumina_fastqs.multiqc.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/read-qc-tools:1.0.1"</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.interactive">
        <b>load_illumina_fastqs.multiqc.interactive</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        ???
</p>
<p name="load_illumina_fastqs.multiqc.machine_mem_gb">
        <b>load_illumina_fastqs.multiqc.machine_mem_gb</b><br />
        <i>Int? &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.run_fastqc">
        <b>load_illumina_fastqs.run_fastqc</b><br />
        <i>Boolean &mdash; Default: true</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.fastqcs">
        <b>load_illumina_fastqs.fastqcs</b><br />
        <i>Array[File]</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_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>

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