4.42. 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.

4.42.1. Inputs

4.42.1.1. Required inputs

find_illumina_files.find_illumina_files_in_directory.illumina_dir
String — Default: None
GCS bucket path to Illumina run directory (e.g., gs://bucket/path/to/run)

4.42.1.2. Advanced inputs

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find_illumina_files.find_illumina_files_in_directory.fastq_dir
String? — Default: None
Override path to fastq files (defaults to {illumina_dir}/fastq)

find_illumina_files.find_illumina_files_in_directory.lane
Int? — Default: None
If specified, filter outputs to only include FASTQs from this sequencing lane number

4.42.1.3. Other inputs

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find_illumina_files.find_illumina_files_in_directory.docker
String — Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-baseimage"
???

4.42.2. Outputs

find_illumina_files.fastqs
Array[String]
???

find_illumina_files.runinfo_xml
String
???

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