# demux_metadata_only
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_metadata_only.biosample_map_tsvs">
        <b>demux_metadata_only.biosample_map_tsvs</b><br />
        <i>Array[File] &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_metadata_only.cleaned_reads_unaligned_bams">
        <b>demux_metadata_only.cleaned_reads_unaligned_bams</b><br />
        <i>Array[File] &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_metadata_only.meta_by_filename_json">
        <b>demux_metadata_only.meta_by_filename_json</b><br />
        <i>File &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_metadata_only.raw_reads_unaligned_bams">
        <b>demux_metadata_only.raw_reads_unaligned_bams</b><br />
        <i>Array[File] &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_metadata_only.run_info">
        <b>demux_metadata_only.run_info</b><br />
        <i>Map[String,String] &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_metadata_only.samplesheets">
        <b>demux_metadata_only.samplesheets</b><br />
        <i>Array[File]+ &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_metadata_only.sra_title">
        <b>demux_metadata_only.sra_title</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>

### Other inputs
<details>
<summary> Show/Hide </summary>
<p name="demux_metadata_only.biosample_map_tsv_join.machine_mem_gb">
        <b>demux_metadata_only.biosample_map_tsv_join.machine_mem_gb</b><br />
        <i>Int &mdash; Default: 7</i><br />
        ???
</p>
<p name="demux_metadata_only.biosample_map_tsv_join.prefer_first">
        <b>demux_metadata_only.biosample_map_tsv_join.prefer_first</b><br />
        <i>Boolean &mdash; Default: true</i><br />
        ???
</p>
<p name="demux_metadata_only.biosample_to_table.docker">
        <b>demux_metadata_only.biosample_to_table.docker</b><br />
        <i>String &mdash; Default: "python:slim"</i><br />
        ???
</p>
<p name="demux_metadata_only.biosample_to_table.sample_table_name">
        <b>demux_metadata_only.biosample_to_table.sample_table_name</b><br />
        <i>String &mdash; Default: "sample"</i><br />
        ???
</p>
<p name="demux_metadata_only.check_terra_env.docker">
        <b>demux_metadata_only.check_terra_env.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="demux_metadata_only.create_or_update_sample_tables.docker">
        <b>demux_metadata_only.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="demux_metadata_only.create_or_update_sample_tables.library_table_name">
        <b>demux_metadata_only.create_or_update_sample_tables.library_table_name</b><br />
        <i>String &mdash; Default: "library"</i><br />
        ???
</p>
<p name="demux_metadata_only.create_or_update_sample_tables.read_counts_cleaned_json">
        <b>demux_metadata_only.create_or_update_sample_tables.read_counts_cleaned_json</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_metadata_only.create_or_update_sample_tables.read_counts_raw_json">
        <b>demux_metadata_only.create_or_update_sample_tables.read_counts_raw_json</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_metadata_only.create_or_update_sample_tables.sample_table_name">
        <b>demux_metadata_only.create_or_update_sample_tables.sample_table_name</b><br />
        <i>String &mdash; Default: "sample"</i><br />
        ???
</p>
<p name="demux_metadata_only.insert_demux_outputs_into_terra_tables">
        <b>demux_metadata_only.insert_demux_outputs_into_terra_tables</b><br />
        <i>Boolean &mdash; Default: false</i><br />
        ???
</p>
<p name="demux_metadata_only.instrument_model_user_specified">
        <b>demux_metadata_only.instrument_model_user_specified</b><br />
        <i>String? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_metadata_only.sample_rename_map">
        <b>demux_metadata_only.sample_rename_map</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="demux_metadata_only.samplesheet_rename_ids.new_id_col">
        <b>demux_metadata_only.samplesheet_rename_ids.new_id_col</b><br />
        <i>String &mdash; Default: 'external_id'</i><br />
        ???
</p>
<p name="demux_metadata_only.samplesheet_rename_ids.old_id_col">
        <b>demux_metadata_only.samplesheet_rename_ids.old_id_col</b><br />
        <i>String &mdash; Default: 'internal_id'</i><br />
        ???
</p>
<p name="demux_metadata_only.sra_meta_prep.docker">
        <b>demux_metadata_only.sra_meta_prep.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="demux_metadata_only.terra_load_biosample_data.docker">
        <b>demux_metadata_only.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_metadata_only.instrument_model_inferred">
        <b>demux_metadata_only.instrument_model_inferred</b><br />
        <i>String</i><br />
        ???
</p>
<p name="demux_metadata_only.sra_metadata">
        <b>demux_metadata_only.sra_metadata</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="demux_metadata_only.terra_library_table">
        <b>demux_metadata_only.terra_library_table</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="demux_metadata_only.terra_sample_library_map">
        <b>demux_metadata_only.terra_sample_library_map</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="demux_metadata_only.terra_sample_metadata">
        <b>demux_metadata_only.terra_sample_metadata</b><br />
        <i>File?</i><br />
        ???
</p>

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> Generated using WDL AID (1.0.0)