# populate_library_and_sample_tables_from_flowcell
Terra only: Populate per-library-lane and per-sample tables from existing demultiplexed flowcell output

## Inputs

### Required inputs
<p name="populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.cleaned_reads_unaligned_bams">
        <b>populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.cleaned_reads_unaligned_bams</b><br />
        <i>Array[String] &mdash; Default: None</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.meta_by_filename_json">
        <b>populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.meta_by_filename_json</b><br />
        <i>File &mdash; Default: None</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.raw_reads_unaligned_bams">
        <b>populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.raw_reads_unaligned_bams</b><br />
        <i>Array[String] &mdash; Default: None</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.flowcell_run_id">
        <b>populate_library_and_sample_tables_from_flowcell.flowcell_run_id</b><br />
        <i>String &mdash; Default: None</i><br />
        ???
</p>

### Other inputs
<details>
<summary> Show/Hide </summary>
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.docker">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.docker">
        <b>populate_library_and_sample_tables_from_flowcell.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="populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.library_table_name">
        <b>populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.library_table_name</b><br />
        <i>String &mdash; Default: "library"</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.read_counts_cleaned_json">
        <b>populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.read_counts_cleaned_json</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.read_counts_raw_json">
        <b>populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.read_counts_raw_json</b><br />
        <i>File? &mdash; Default: None</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.sample_table_name">
        <b>populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.sample_table_name</b><br />
        <i>String &mdash; Default: "sample"</i><br />
        ???
</p>
</details>

## Outputs
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.env_info">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.env_info</b><br />
        <i>File</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.gcloud_config_info">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.gcloud_config_info</b><br />
        <i>File</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.gcp_instance_metadata">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.gcp_instance_metadata</b><br />
        <i>File</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.google_project_id">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.google_project_id</b><br />
        <i>String</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.input_row_id">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.input_row_id</b><br />
        <i>String</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.input_table_name">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.input_table_name</b><br />
        <i>String</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.is_backed_by_gcp">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.is_backed_by_gcp</b><br />
        <i>Boolean</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.is_running_on_terra">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.is_running_on_terra</b><br />
        <i>Boolean</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.is_running_via_gcp_batch">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.is_running_via_gcp_batch</b><br />
        <i>Boolean</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.is_running_via_gcp_papiv2">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.is_running_via_gcp_papiv2</b><br />
        <i>Boolean</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.max_ram_gb">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.max_ram_gb</b><br />
        <i>Int</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.method_path">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.method_path</b><br />
        <i>String</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.method_source">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.method_source</b><br />
        <i>String</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.method_version">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.method_version</b><br />
        <i>String</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.top_level_submission_id">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.top_level_submission_id</b><br />
        <i>String</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.user_email">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.user_email</b><br />
        <i>String</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.workspace_bucket_path">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.workspace_bucket_path</b><br />
        <i>String</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.workspace_name">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.workspace_name</b><br />
        <i>String</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.workspace_namespace">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.workspace_namespace</b><br />
        <i>String</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.check_terra_env.workspace_uuid">
        <b>populate_library_and_sample_tables_from_flowcell.check_terra_env.workspace_uuid</b><br />
        <i>String</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.library_bams_tsv">
        <b>populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.library_bams_tsv</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.library_metadata_tsv">
        <b>populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.library_metadata_tsv</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.max_ram_gb">
        <b>populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.max_ram_gb</b><br />
        <i>Int?</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.sample_membership_tsv">
        <b>populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.sample_membership_tsv</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.stderr_log">
        <b>populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.stderr_log</b><br />
        <i>File?</i><br />
        ???
</p>
<p name="populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.stdout_log">
        <b>populate_library_and_sample_tables_from_flowcell.create_or_update_sample_tables.stdout_log</b><br />
        <i>File?</i><br />
        ???
</p>

<hr />

> Generated using WDL AID (1.0.0)