# find_illumina_files
Utility workflow to discover and structure Illumina run files from a GCS bucket directory. This workflow uses gcloud storage commands and is only compatible with Google Cloud Platform.

## Inputs

### Required inputs
<p name="find_illumina_files.find_illumina_files_in_directory.illumina_dir">
        <b>find_illumina_files.find_illumina_files_in_directory.illumina_dir</b><br />
        <i>String &mdash; Default: None</i><br />
        GCS bucket path to Illumina run directory (e.g., gs://bucket/path/to/run)
</p>

### Advanced inputs
<details>
<summary> Show/Hide </summary>
<p name="find_illumina_files.find_illumina_files_in_directory.fastq_dir">
        <b>find_illumina_files.find_illumina_files_in_directory.fastq_dir</b><br />
        <i>String? &mdash; Default: None</i><br />
        Override path to fastq files (defaults to {illumina_dir}/fastq)
</p>
<p name="find_illumina_files.find_illumina_files_in_directory.lane">
        <b>find_illumina_files.find_illumina_files_in_directory.lane</b><br />
        <i>Int? &mdash; Default: None</i><br />
        If specified, filter outputs to only include FASTQs from this sequencing lane number
</p>
</details>

### Other inputs
<details>
<summary> Show/Hide </summary>
<p name="find_illumina_files.find_illumina_files_in_directory.docker">
        <b>find_illumina_files.find_illumina_files_in_directory.docker</b><br />
        <i>String &mdash; Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-baseimage"</i><br />
        ???
</p>
</details>

## Outputs
<p name="find_illumina_files.fastqs">
        <b>find_illumina_files.fastqs</b><br />
        <i>Array[String]</i><br />
        ???
</p>
<p name="find_illumina_files.runinfo_xml">
        <b>find_illumina_files.runinfo_xml</b><br />
        <i>String</i><br />
        ???
</p>

<hr />

> Generated using WDL AID (1.0.0)