# demux_deplete
Picard-based demultiplexing and basecalling from a tarball of a raw BCL directory, followed by QC metrics, depletion, and SRA submission prep.

## Inputs

### Required inputs
<p name="demux_deplete.flowcell_tgz">
        <b>demux_deplete.flowcell_tgz</b><br />
        <i>File &mdash; Default: None</i><br />
        Illumina BCL directory compressed as tarball. Must contain RunInfo.xml, SampleSheet.csv, RTAComplete.txt, and Data/Intensities/BaseCalls/*
</p>
<p name="demux_deplete.samplesheets">
        <b>demux_deplete.samplesheets</b><br />
        <i>Array[File]+ &mdash; Default: None</i><br />
        Custom formatted 'extended' format tsv samplesheets that will override any SampleSheet.csv in the illumina BCL directory. Must supply one file per lane of the flowcell, and must provide them in lane order. Required tsv column headings are: sample, library_id_per_sample, barcode_1, barcode_2 (if paired reads, omit if single-end), barcode_3 (if additional demultiplexing downstream by other means, otherwise may be omitted), library_strategy, library_source, library_selection, design_description. 'sample' must correspond to a biological sample. ('sample' x 'library_id_per_sample') must be unique within a samplesheet and correspond to independent libraries from the same original sample. barcode_1 and barcode_2 must correspond to the actual index sequences. Remaining columns must follow strict ontology: see 3rd tab of https://www.ncbi.nlm.nih.gov/core/assets/sra/files/SRA_metadata_acc_example.xlsx for controlled vocabulary and term definitions.
</p>
<p name="demux_deplete.spikein_db">
        <b>demux_deplete.spikein_db</b><br />
        <i>File &mdash; Default: None</i><br />
        Synthetic sequences (e.g. ERCC, SDSI) that are used to track potential contamination within sequencing plate processing.
</p>

### Advanced inputs
<details>
<summary> Show/Hide </summary>
<p name="demux_deplete.biosample_map_tsvs">
        <b>demux_deplete.biosample_map_tsvs</b><br />
        <i>Array[File] &mdash; Default: []</i><br />
        One or more tsv files, each containing at least the following columns: 'sample_name', 'accession'. 'sample_name' refers to the external sample id, 'accession' is the NCBI BioSample accession (SAMN########). Recommended input: the BioSample attributes tsv returned by NCBI following successful submission of a new list of BioSample attributes. If this file is omitted, SRA submission prep will be skipped.
</p>
<p name="demux_deplete.bmtaggerDbs">
        <b>demux_deplete.bmtaggerDbs</b><br />
        <i>Array[File]? &mdash; Default: None</i><br />
        Tool that can discriminate between human and bacterial reads and other reads by using short fragments. Databases must be provided to onset depletion.Sequences in fasta format will be indexed on the fly, pre-bmtagger-indexed databases may be provided as tarballs.
</p>
<p name="demux_deplete.illumina_demux.barcode_columns_to_rev_comp">
        <b>demux_deplete.illumina_demux.barcode_columns_to_rev_comp</b><br />
        <i>Array[String]? &mdash; Default: None</i><br />
        Columns in the sample sheet to reverse-complement. Only used if 'rev_comp_barcodes_before_demux' is true. Defaults to 'barcode_2'.
</p>
<p name="demux_deplete.illumina_demux.rev_comp_barcodes_before_demux">
        <b>demux_deplete.illumina_demux.rev_comp_barcodes_before_demux</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        Reverse-complement the barcode(s) before demultiplexing. By default, this action applies to values in the 'barcode_2' column unless overridden by 'barcode_columns_to_rev_comp'.
</p>
<p name="demux_deplete.illumina_demux.runinfo">
        <b>demux_deplete.illumina_demux.runinfo</b><br />
        <i>File? &mdash; Default: None</i><br />
        if we are overriding the RunInfo file, use the path of the file provided. Otherwise the default will be RunInfo.xml. 
</p>
<p name="demux_deplete.insert_demux_outputs_into_terra_tables">
        <b>demux_deplete.insert_demux_outputs_into_terra_tables</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        Terra only: if set to 'true', demux output will be used to insert entries in 'library' (per library-lane) and 'sample tables' (referencing one or more libraries per sample ID)
</p>
<p name="demux_deplete.read_structure">
        <b>demux_deplete.read_structure</b><br />
        <i>String? &mdash; Default: None</i><br />
        Details how the bases should be organized into logical reads.
</p>
<p name="demux_deplete.sample_rename_map">
        <b>demux_deplete.sample_rename_map</b><br />
        <i>File? &mdash; Default: None</i><br />
        If 'samples' need to be renamed, provide a two-column tsv that contains at least the following columns: 'internal_id', 'external_id'. All samples will be renamed prior to analysis. Any samples described in the samplesheets that are not present in sample_rename_map will be unaltered. If this is omitted, no samples will be renamed.
</p>
<p name="demux_deplete.sort_reads">
        <b>demux_deplete.sort_reads</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        Output bam files will be sorted by read name.
</p>
</details>

### Other inputs
<details>
<summary> Show/Hide </summary>
<p name="demux_deplete.biosample_map_tsv_join.machine_mem_gb">
        <b>demux_deplete.biosample_map_tsv_join.machine_mem_gb</b><br />
        <i>Int &mdash; Default: 7</i><br />
        ???
</p>
<p name="demux_deplete.biosample_map_tsv_join.prefer_first">
        <b>demux_deplete.biosample_map_tsv_join.prefer_first</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        ???
</p>
<p name="demux_deplete.biosample_to_table.docker">
        <b>demux_deplete.biosample_to_table.docker</b><br />
        <i>String &mdash; Default: "python:slim"</i><br />
        ???
</p>
<p name="demux_deplete.biosample_to_table.sample_table_name">
        <b>demux_deplete.biosample_to_table.sample_table_name</b><br />
        <i>String &mdash; Default: "sample"</i><br />
        ???
</p>
<p name="demux_deplete.blastDbs">
        <b>demux_deplete.blastDbs</b><br />
        <i>Array[File]? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.bwaDbs">
        <b>demux_deplete.bwaDbs</b><br />
        <i>Array[File]? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.check_terra_env.docker">
        <b>demux_deplete.check_terra_env.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-core:2.5.21"</i><br />
        ???
</p>
<p name="demux_deplete.create_or_update_sample_tables.docker">
        <b>demux_deplete.create_or_update_sample_tables.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-core:2.5.21"</i><br />
        ???
</p>
<p name="demux_deplete.create_or_update_sample_tables.library_table_name">
        <b>demux_deplete.create_or_update_sample_tables.library_table_name</b><br />
        <i>String &mdash; Default: "library"</i><br />
        ???
</p>
<p name="demux_deplete.create_or_update_sample_tables.sample_table_name">
        <b>demux_deplete.create_or_update_sample_tables.sample_table_name</b><br />
        <i>String &mdash; Default: "sample"</i><br />
        ???
</p>
<p name="demux_deplete.default_filename_keys">
        <b>demux_deplete.default_filename_keys</b><br />
        <i>Array[String] &mdash; Default: ["spike_in", "batch_lib"]</i><br />
        ???
</p>
<p name="demux_deplete.default_sample_keys">
        <b>demux_deplete.default_sample_keys</b><br />
        <i>Array[String] &mdash; Default: ["amplicon_set", "control", "batch_lib", "viral_ct"]</i><br />
        ???
</p>
<p name="demux_deplete.deplete.clear_tags">
        <b>demux_deplete.deplete.clear_tags</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="demux_deplete.deplete.cpu">
        <b>demux_deplete.deplete.cpu</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.deplete.docker">
        <b>demux_deplete.deplete.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-classify:2.5.21.1"</i><br />
        ???
</p>
<p name="demux_deplete.deplete.machine_mem_gb">
        <b>demux_deplete.deplete.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.deplete.query_chunk_size">
        <b>demux_deplete.deplete.query_chunk_size</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.deplete.tags_to_clear_space_separated">
        <b>demux_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="demux_deplete.illumina_demux.disk_size">
        <b>demux_deplete.illumina_demux.disk_size</b><br />
        <i>Int &mdash; Default: 3000</i><br />
        ???
</p>
<p name="demux_deplete.illumina_demux.docker">
        <b>demux_deplete.illumina_demux.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-core:2.5.21"</i><br />
        ???
</p>
<p name="demux_deplete.illumina_demux.emit_unmatched_reads_bam">
        <b>demux_deplete.illumina_demux.emit_unmatched_reads_bam</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="demux_deplete.illumina_demux.firstTile">
        <b>demux_deplete.illumina_demux.firstTile</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.illumina_demux.flowcell">
        <b>demux_deplete.illumina_demux.flowcell</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.illumina_demux.inner_barcode_predemux_trim_r1_3prime">
        <b>demux_deplete.illumina_demux.inner_barcode_predemux_trim_r1_3prime</b><br />
        <i>Int &mdash; Default: 18</i><br />
        ???
</p>
<p name="demux_deplete.illumina_demux.inner_barcode_predemux_trim_r2_3prime">
        <b>demux_deplete.illumina_demux.inner_barcode_predemux_trim_r2_3prime</b><br />
        <i>Int &mdash; Default: 18</i><br />
        ???
</p>
<p name="demux_deplete.illumina_demux.inner_barcode_predemux_trim_r2_5prime">
        <b>demux_deplete.illumina_demux.inner_barcode_predemux_trim_r2_5prime</b><br />
        <i>Int &mdash; Default: 18</i><br />
        ???
</p>
<p name="demux_deplete.illumina_demux.inner_barcode_trim_r1_right_of_barcode">
        <b>demux_deplete.illumina_demux.inner_barcode_trim_r1_right_of_barcode</b><br />
        <i>Int &mdash; Default: 10</i><br />
        ???
</p>
<p name="demux_deplete.illumina_demux.machine_mem_gb">
        <b>demux_deplete.illumina_demux.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.illumina_demux.maxMismatches">
        <b>demux_deplete.illumina_demux.maxMismatches</b><br />
        <i>Int? &mdash; Default: 0</i><br />
        ???
</p>
<p name="demux_deplete.illumina_demux.maxNoCalls">
        <b>demux_deplete.illumina_demux.maxNoCalls</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.illumina_demux.maxRecordsInRam">
        <b>demux_deplete.illumina_demux.maxRecordsInRam</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.illumina_demux.minimumBaseQuality">
        <b>demux_deplete.illumina_demux.minimumBaseQuality</b><br />
        <i>Int? &mdash; Default: 10</i><br />
        ???
</p>
<p name="demux_deplete.illumina_demux.minimumQuality">
        <b>demux_deplete.illumina_demux.minimumQuality</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.illumina_demux.minMismatchDelta">
        <b>demux_deplete.illumina_demux.minMismatchDelta</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.illumina_demux.numberOfNegativeControls">
        <b>demux_deplete.illumina_demux.numberOfNegativeControls</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.illumina_demux.runStartDate">
        <b>demux_deplete.illumina_demux.runStartDate</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.illumina_demux.sequencingCenter">
        <b>demux_deplete.illumina_demux.sequencingCenter</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.illumina_demux.threads">
        <b>demux_deplete.illumina_demux.threads</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.illumina_demux.tileLimit">
        <b>demux_deplete.illumina_demux.tileLimit</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.instrument_model_user_specified">
        <b>demux_deplete.instrument_model_user_specified</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.min_reads_per_bam">
        <b>demux_deplete.min_reads_per_bam</b><br />
        <i>Int &mdash; Default: 100</i><br />
        ???
</p>
<p name="demux_deplete.minimapDbs">
        <b>demux_deplete.minimapDbs</b><br />
        <i>Array[File]? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_cleaned.comment">
        <b>demux_deplete.multiqc_cleaned.comment</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_cleaned.config">
        <b>demux_deplete.multiqc_cleaned.config</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_cleaned.config_yaml">
        <b>demux_deplete.multiqc_cleaned.config_yaml</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_cleaned.cpu">
        <b>demux_deplete.multiqc_cleaned.cpu</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_cleaned.disk_size_gb">
        <b>demux_deplete.multiqc_cleaned.disk_size_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_cleaned.docker">
        <b>demux_deplete.multiqc_cleaned.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/read-qc-tools:1.0.1"</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_cleaned.full_names">
        <b>demux_deplete.multiqc_cleaned.full_names</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_cleaned.interactive">
        <b>demux_deplete.multiqc_cleaned.interactive</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_cleaned.machine_mem_gb">
        <b>demux_deplete.multiqc_cleaned.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_cleaned.title">
        <b>demux_deplete.multiqc_cleaned.title</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_raw.comment">
        <b>demux_deplete.multiqc_raw.comment</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_raw.config">
        <b>demux_deplete.multiqc_raw.config</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_raw.config_yaml">
        <b>demux_deplete.multiqc_raw.config_yaml</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_raw.cpu">
        <b>demux_deplete.multiqc_raw.cpu</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_raw.disk_size_gb">
        <b>demux_deplete.multiqc_raw.disk_size_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_raw.docker">
        <b>demux_deplete.multiqc_raw.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/read-qc-tools:1.0.1"</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_raw.full_names">
        <b>demux_deplete.multiqc_raw.full_names</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_raw.interactive">
        <b>demux_deplete.multiqc_raw.interactive</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_raw.machine_mem_gb">
        <b>demux_deplete.multiqc_raw.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_raw.title">
        <b>demux_deplete.multiqc_raw.title</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.revcomp_i5.docker">
        <b>demux_deplete.revcomp_i5.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/py3-bio:0.1.3"</i><br />
        ???
</p>
<p name="demux_deplete.revcomp_i5.revcomp">
        <b>demux_deplete.revcomp_i5.revcomp</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        ???
</p>
<p name="demux_deplete.revcomp_i5_indexes">
        <b>demux_deplete.revcomp_i5_indexes</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="demux_deplete.samplesheet_rename_ids.new_id_col">
        <b>demux_deplete.samplesheet_rename_ids.new_id_col</b><br />
        <i>String &mdash; Default: 'external_id'</i><br />
        ???
</p>
<p name="demux_deplete.samplesheet_rename_ids.old_id_col">
        <b>demux_deplete.samplesheet_rename_ids.old_id_col</b><br />
        <i>String &mdash; Default: 'internal_id'</i><br />
        ???
</p>
<p name="demux_deplete.spike_summary.docker">
        <b>demux_deplete.spike_summary.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-core:2.5.21"</i><br />
        ???
</p>
<p name="demux_deplete.spike_summary.output_prefix">
        <b>demux_deplete.spike_summary.output_prefix</b><br />
        <i>String &mdash; Default: "count_summary"</i><br />
        ???
</p>
<p name="demux_deplete.spikein.cpu">
        <b>demux_deplete.spikein.cpu</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.spikein.docker">
        <b>demux_deplete.spikein.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-core:2.5.21"</i><br />
        ???
</p>
<p name="demux_deplete.spikein.machine_mem_gb">
        <b>demux_deplete.spikein.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.spikein.topNHits">
        <b>demux_deplete.spikein.topNHits</b><br />
        <i>Int &mdash; Default: 3</i><br />
        ???
</p>
<p name="demux_deplete.sra_meta_prep.docker">
        <b>demux_deplete.sra_meta_prep.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-core:2.5.21"</i><br />
        ???
</p>
<p name="demux_deplete.sra_title">
        <b>demux_deplete.sra_title</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_deplete.terra_load_biosample_data.docker">
        <b>demux_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="demux_deplete.cleaned_bam_uris">
        <b>demux_deplete.cleaned_bam_uris</b><br />
        <i>File?</i><br />
        A text file containing a string-serialized version of each File in cleaned_reads_unaligned_bams on a separate line.
</p>
<p name="demux_deplete.cleaned_bams_tiny">
        <b>demux_deplete.cleaned_bams_tiny</b><br />
        <i>Array[File]</i><br />
        cleaned BAM files that contain less than min_reads_per_bam will be included here and omitted from cleaned_reads_unaligned_bams and cleaned_bam_uris
</p>
<p name="demux_deplete.cleaned_reads_unaligned_bams">
        <b>demux_deplete.cleaned_reads_unaligned_bams</b><br />
        <i>Array[File]</i><br />
        Unaligned reads without human reads or PCR duplicates in BAM format. This will not include any bams that contain less than min_reads_per_bam reads.
</p>
<p name="demux_deplete.demux_commonBarcodes">
        <b>demux_deplete.demux_commonBarcodes</b><br />
        <i>Array[File]</i><br />
        a TSV report of all barcode counts, in descending order.
</p>
<p name="demux_deplete.demux_metrics">
        <b>demux_deplete.demux_metrics</b><br />
        <i>Array[File]</i><br />
        Output ExtractIlluminaBarcodes metrics file.
</p>
<p name="demux_deplete.demux_outlierBarcodes">
        <b>demux_deplete.demux_outlierBarcodes</b><br />
        <i>Array[File]</i><br />
        ???
</p>
<p name="demux_deplete.demux_viral_core_version">
        <b>demux_deplete.demux_viral_core_version</b><br />
        <i>String</i><br />
        ???
</p>
<p name="demux_deplete.instrument_model_inferred">
        <b>demux_deplete.instrument_model_inferred</b><br />
        <i>String</i><br />
        ???
</p>
<p name="demux_deplete.meta_by_filename">
        <b>demux_deplete.meta_by_filename</b><br />
        <i>Map[String,Map[String,String]]</i><br />
        ???
</p>
<p name="demux_deplete.meta_by_filename_json">
        <b>demux_deplete.meta_by_filename_json</b><br />
        <i>File</i><br />
        ???
</p>
<p name="demux_deplete.meta_by_sample">
        <b>demux_deplete.meta_by_sample</b><br />
        <i>Map[String,Map[String,String]]</i><br />
        ???
</p>
<p name="demux_deplete.meta_by_sample_json">
        <b>demux_deplete.meta_by_sample_json</b><br />
        <i>File</i><br />
        ???
</p>
<p name="demux_deplete.multiqc_report_cleaned">
        <b>demux_deplete.multiqc_report_cleaned</b><br />
        <i>File</i><br />
        Aggregate results from QC analyses across many samples into a single report.
</p>
<p name="demux_deplete.multiqc_report_raw">
        <b>demux_deplete.multiqc_report_raw</b><br />
        <i>File</i><br />
        ???
</p>
<p name="demux_deplete.raw_reads_unaligned_bams">
        <b>demux_deplete.raw_reads_unaligned_bams</b><br />
        <i>Array[File]</i><br />
        Unaligned reads in BAM format.
</p>
<p name="demux_deplete.read_counts_depleted">
        <b>demux_deplete.read_counts_depleted</b><br />
        <i>Array[Int]</i><br />
        ???
</p>
<p name="demux_deplete.read_counts_raw">
        <b>demux_deplete.read_counts_raw</b><br />
        <i>Array[Int]</i><br />
        A list of the read counts of each file in raw_reads_unaligned_bams
</p>
<p name="demux_deplete.run_date">
        <b>demux_deplete.run_date</b><br />
        <i>String</i><br />
        ???
</p>
<p name="demux_deplete.run_id">
        <b>demux_deplete.run_id</b><br />
        <i>String</i><br />
        ???
</p>
<p name="demux_deplete.run_info">
        <b>demux_deplete.run_info</b><br />
        <i>Map[String,String]</i><br />
        ???
</p>
<p name="demux_deplete.run_info_json">
        <b>demux_deplete.run_info_json</b><br />
        <i>File</i><br />
        ???
</p>
<p name="demux_deplete.spikein_counts">
        <b>demux_deplete.spikein_counts</b><br />
        <i>File</i><br />
        ???
</p>
<p name="demux_deplete.sra_metadata">
        <b>demux_deplete.sra_metadata</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="demux_deplete.terra_library_table">
        <b>demux_deplete.terra_library_table</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="demux_deplete.terra_sample_library_map">
        <b>demux_deplete.terra_sample_library_map</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="demux_deplete.terra_sample_metadata">
        <b>demux_deplete.terra_sample_metadata</b><br />
        <i>File?</i><br />
        ???
</p>

<hr />

> Generated using WDL AID (1.0.0)