download_project.py¶
Downloads a SCGPM sequencing results project from DNAnexus. Currently, there is one DNAnexus project for each lane of Illumina sequencing. A folder will be created by the name of the DNAnexus project within the specified output folder. The project folder will contain a FASTQ subfolder, a FASTQC subfolder, and several files including 1) the sequencing QC report, 2) the list of barcodes in the sequencing lane in barcodes.json, run information in run_details.json, and a meta-data tarball by the name of ${sequencing_run_name}.metadata.tar. This last file contains important XML files output by the sequencer, such as the runParameters.XML and RunInfo.xml.
usage: download_project.py [-h] --download-dir DOWNLOAD_DIR
(--dx-project-id DX_PROJECT_ID | --dx-project-list DX_PROJECT_LIST)
Named Arguments¶
| --download-dir |
|
| --dx-project-id | |
| The DNAnexus ID of the project to download. | |
| --dx-project-list | |
| |