# load_illumina_fastqs_deplete
Process DRAGEN FASTQ files into per-sample BAM files with demultiplexing, depletion, and SRA submission prep.

## Inputs

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

### Advanced inputs
<details>
<summary> Show/Hide </summary>
<p name="load_illumina_fastqs_deplete.get_illumina_run_metadata.sequencing_center">
        <b>load_illumina_fastqs_deplete.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_deplete.biosample_map_tsv_join.machine_mem_gb">
        <b>load_illumina_fastqs_deplete.biosample_map_tsv_join.machine_mem_gb</b><br />
        <i>Int &mdash; Default: 7</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.biosample_map_tsv_join.prefer_first">
        <b>load_illumina_fastqs_deplete.biosample_map_tsv_join.prefer_first</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.biosample_map_tsvs">
        <b>load_illumina_fastqs_deplete.biosample_map_tsvs</b><br />
        <i>Array[File] &mdash; Default: []</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.biosample_to_table.docker">
        <b>load_illumina_fastqs_deplete.biosample_to_table.docker</b><br />
        <i>String &mdash; Default: "python:slim"</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.biosample_to_table.sample_table_name">
        <b>load_illumina_fastqs_deplete.biosample_to_table.sample_table_name</b><br />
        <i>String &mdash; Default: "sample"</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.blastDbs">
        <b>load_illumina_fastqs_deplete.blastDbs</b><br />
        <i>Array[File]? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.bmtaggerDbs">
        <b>load_illumina_fastqs_deplete.bmtaggerDbs</b><br />
        <i>Array[File]? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.bwaDbs">
        <b>load_illumina_fastqs_deplete.bwaDbs</b><br />
        <i>Array[File]? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.check_for_barcode3.docker">
        <b>load_illumina_fastqs_deplete.check_for_barcode3.docker</b><br />
        <i>String &mdash; Default: "python:slim"</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.check_terra_env.docker">
        <b>load_illumina_fastqs_deplete.check_terra_env.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.create_or_update_sample_tables.docker">
        <b>load_illumina_fastqs_deplete.create_or_update_sample_tables.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.create_or_update_sample_tables.library_table_name">
        <b>load_illumina_fastqs_deplete.create_or_update_sample_tables.library_table_name</b><br />
        <i>String &mdash; Default: "library"</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.create_or_update_sample_tables.sample_table_name">
        <b>load_illumina_fastqs_deplete.create_or_update_sample_tables.sample_table_name</b><br />
        <i>String &mdash; Default: "sample"</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.default_filename_keys">
        <b>load_illumina_fastqs_deplete.default_filename_keys</b><br />
        <i>Array[String] &mdash; Default: ["spike_in", "batch_lib"]</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.default_sample_keys">
        <b>load_illumina_fastqs_deplete.default_sample_keys</b><br />
        <i>Array[String] &mdash; Default: ["amplicon_set", "control", "batch_lib", "viral_ct"]</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.demux_fastqs.cpu">
        <b>load_illumina_fastqs_deplete.demux_fastqs.cpu</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.demux_fastqs.disk_size">
        <b>load_illumina_fastqs_deplete.demux_fastqs.disk_size</b><br />
        <i>Int &mdash; Default: 750</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.demux_fastqs.docker">
        <b>load_illumina_fastqs_deplete.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_deplete.demux_fastqs.machine_mem_gb">
        <b>load_illumina_fastqs_deplete.demux_fastqs.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.demux_fastqs.sequencingCenter">
        <b>load_illumina_fastqs_deplete.demux_fastqs.sequencingCenter</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.demux_max_cpu_no_splitcode">
        <b>load_illumina_fastqs_deplete.demux_max_cpu_no_splitcode</b><br />
        <i>Int &mdash; Default: 16</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.demux_max_cpu_splitcode">
        <b>load_illumina_fastqs_deplete.demux_max_cpu_splitcode</b><br />
        <i>Int &mdash; Default: 64</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.deplete.clear_tags">
        <b>load_illumina_fastqs_deplete.deplete.clear_tags</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.deplete.cpu">
        <b>load_illumina_fastqs_deplete.deplete.cpu</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.deplete.docker">
        <b>load_illumina_fastqs_deplete.deplete.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-classify"</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.deplete.machine_mem_gb">
        <b>load_illumina_fastqs_deplete.deplete.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.deplete.query_chunk_size">
        <b>load_illumina_fastqs_deplete.deplete.query_chunk_size</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.deplete.tags_to_clear_space_separated">
        <b>load_illumina_fastqs_deplete.deplete.tags_to_clear_space_separated</b><br />
        <i>String &mdash; Default: "XT X0 X1 XA AM SM BQ CT XN OC OP"</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.get_illumina_run_metadata.docker">
        <b>load_illumina_fastqs_deplete.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_deplete.get_illumina_run_metadata.machine_mem_gb">
        <b>load_illumina_fastqs_deplete.get_illumina_run_metadata.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.insert_demux_outputs_into_terra_tables">
        <b>load_illumina_fastqs_deplete.insert_demux_outputs_into_terra_tables</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.instrument_model_user_specified">
        <b>load_illumina_fastqs_deplete.instrument_model_user_specified</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.merge_demux_metrics.docker">
        <b>load_illumina_fastqs_deplete.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_deplete.merge_sample_metadata.out_meta_by_filename">
        <b>load_illumina_fastqs_deplete.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_deplete.merge_sample_metadata.out_meta_by_sample">
        <b>load_illumina_fastqs_deplete.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_deplete.min_reads_per_bam">
        <b>load_illumina_fastqs_deplete.min_reads_per_bam</b><br />
        <i>Int &mdash; Default: 100</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.minimapDbs">
        <b>load_illumina_fastqs_deplete.minimapDbs</b><br />
        <i>Array[File]? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_cleaned.comment">
        <b>load_illumina_fastqs_deplete.multiqc_cleaned.comment</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_cleaned.config">
        <b>load_illumina_fastqs_deplete.multiqc_cleaned.config</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_cleaned.config_yaml">
        <b>load_illumina_fastqs_deplete.multiqc_cleaned.config_yaml</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_cleaned.cpu">
        <b>load_illumina_fastqs_deplete.multiqc_cleaned.cpu</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_cleaned.disk_size_gb">
        <b>load_illumina_fastqs_deplete.multiqc_cleaned.disk_size_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_cleaned.docker">
        <b>load_illumina_fastqs_deplete.multiqc_cleaned.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/read-qc-tools:1.0.1"</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_cleaned.full_names">
        <b>load_illumina_fastqs_deplete.multiqc_cleaned.full_names</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_cleaned.interactive">
        <b>load_illumina_fastqs_deplete.multiqc_cleaned.interactive</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_cleaned.machine_mem_gb">
        <b>load_illumina_fastqs_deplete.multiqc_cleaned.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_cleaned.title">
        <b>load_illumina_fastqs_deplete.multiqc_cleaned.title</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_raw.comment">
        <b>load_illumina_fastqs_deplete.multiqc_raw.comment</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_raw.config">
        <b>load_illumina_fastqs_deplete.multiqc_raw.config</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_raw.config_yaml">
        <b>load_illumina_fastqs_deplete.multiqc_raw.config_yaml</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_raw.cpu">
        <b>load_illumina_fastqs_deplete.multiqc_raw.cpu</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_raw.disk_size_gb">
        <b>load_illumina_fastqs_deplete.multiqc_raw.disk_size_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_raw.docker">
        <b>load_illumina_fastqs_deplete.multiqc_raw.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/read-qc-tools:1.0.1"</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_raw.full_names">
        <b>load_illumina_fastqs_deplete.multiqc_raw.full_names</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_raw.interactive">
        <b>load_illumina_fastqs_deplete.multiqc_raw.interactive</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_raw.machine_mem_gb">
        <b>load_illumina_fastqs_deplete.multiqc_raw.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_raw.title">
        <b>load_illumina_fastqs_deplete.multiqc_raw.title</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.run_fastqc">
        <b>load_illumina_fastqs_deplete.run_fastqc</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.sample_rename_map">
        <b>load_illumina_fastqs_deplete.sample_rename_map</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.samplesheet_rename_ids.new_id_col">
        <b>load_illumina_fastqs_deplete.samplesheet_rename_ids.new_id_col</b><br />
        <i>String &mdash; Default: 'external_id'</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.samplesheet_rename_ids.old_id_col">
        <b>load_illumina_fastqs_deplete.samplesheet_rename_ids.old_id_col</b><br />
        <i>String &mdash; Default: 'internal_id'</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.spike_summary.docker">
        <b>load_illumina_fastqs_deplete.spike_summary.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.spike_summary.output_prefix">
        <b>load_illumina_fastqs_deplete.spike_summary.output_prefix</b><br />
        <i>String &mdash; Default: "count_summary"</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.spikein.cpu">
        <b>load_illumina_fastqs_deplete.spikein.cpu</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.spikein.docker">
        <b>load_illumina_fastqs_deplete.spikein.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.spikein.machine_mem_gb">
        <b>load_illumina_fastqs_deplete.spikein.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.spikein.topNHits">
        <b>load_illumina_fastqs_deplete.spikein.topNHits</b><br />
        <i>Int &mdash; Default: 3</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.spikein_db">
        <b>load_illumina_fastqs_deplete.spikein_db</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.sra_meta_prep.docker">
        <b>load_illumina_fastqs_deplete.sra_meta_prep.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.sra_title">
        <b>load_illumina_fastqs_deplete.sra_title</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.terra_load_biosample_data.docker">
        <b>load_illumina_fastqs_deplete.terra_load_biosample_data.docker</b><br />
        <i>String &mdash; Default: "schaluvadi/pathogen-genomic-surveillance:api-wdl"</i><br />
        ???
</p>
</details>

## Outputs
<p name="load_illumina_fastqs_deplete.cleaned_bam_uris">
        <b>load_illumina_fastqs_deplete.cleaned_bam_uris</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.cleaned_bams_tiny">
        <b>load_illumina_fastqs_deplete.cleaned_bams_tiny</b><br />
        <i>Array[File]</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.cleaned_reads_unaligned_bams">
        <b>load_illumina_fastqs_deplete.cleaned_reads_unaligned_bams</b><br />
        <i>Array[File]</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.demux_metrics">
        <b>load_illumina_fastqs_deplete.demux_metrics</b><br />
        <i>File</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.fastqcs_cleaned">
        <b>load_illumina_fastqs_deplete.fastqcs_cleaned</b><br />
        <i>Array[File]</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.fastqcs_raw">
        <b>load_illumina_fastqs_deplete.fastqcs_raw</b><br />
        <i>Array[File]</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.instrument_model_inferred">
        <b>load_illumina_fastqs_deplete.instrument_model_inferred</b><br />
        <i>String</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.meta_by_filename_json">
        <b>load_illumina_fastqs_deplete.meta_by_filename_json</b><br />
        <i>File</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.meta_by_sample_json">
        <b>load_illumina_fastqs_deplete.meta_by_sample_json</b><br />
        <i>File</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_report_cleaned">
        <b>load_illumina_fastqs_deplete.multiqc_report_cleaned</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.multiqc_report_raw">
        <b>load_illumina_fastqs_deplete.multiqc_report_raw</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.raw_reads_unaligned_bams">
        <b>load_illumina_fastqs_deplete.raw_reads_unaligned_bams</b><br />
        <i>Array[File]</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.read_counts_depleted">
        <b>load_illumina_fastqs_deplete.read_counts_depleted</b><br />
        <i>Array[Int]</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.read_counts_raw">
        <b>load_illumina_fastqs_deplete.read_counts_raw</b><br />
        <i>Array[Int]</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.run_info">
        <b>load_illumina_fastqs_deplete.run_info</b><br />
        <i>Map[String,String]</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.run_info_json">
        <b>load_illumina_fastqs_deplete.run_info_json</b><br />
        <i>File</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.spikein_counts">
        <b>load_illumina_fastqs_deplete.spikein_counts</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.sra_metadata">
        <b>load_illumina_fastqs_deplete.sra_metadata</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.terra_library_table">
        <b>load_illumina_fastqs_deplete.terra_library_table</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.terra_sample_library_map">
        <b>load_illumina_fastqs_deplete.terra_sample_library_map</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.terra_sample_metadata">
        <b>load_illumina_fastqs_deplete.terra_sample_metadata</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="load_illumina_fastqs_deplete.viralngs_version">
        <b>load_illumina_fastqs_deplete.viralngs_version</b><br />
        <i>String</i><br />
        ???
</p>

<hr />

> Generated using WDL AID (1.0.0)