download_fastqs.py

To fill in.

usage: download_fastqs.py [-h] --errlog ERRLOG [-l LIBRARY_NAME]
                          [--uhts-run-name UHTS_RUN_NAME]
                          [--dx-project-name DX_PROJECT_NAME] [--lane LANE]
                          [-b BARCODE [BARCODE ...]] -d FILE_DOWNLOAD_DIR
                          [--not-found-error]

Named Arguments

--errlog	Log file name to write errors to (i.e. When a DNAnexus project isn’t found). Will be opened in append mode.
-l, --library-name
	The library name of the sample that was sequenced. This is name of the library that was submitted to SCGPM for sequencing. This is added as a property to all sequencing result projects through the ‘library_name’ project property.
--uhts-run-name
	The name of the sequencing run in UHTS. This is added as a property to all projects in DNAnexus through the ‘seq_run_name’ project property. Use this option in combination with –library-name and –lane to further restrict the search space, which is useful especially since multiple DNAnexus projects can have the same library_name property value (i.e. if resequencing the same library).
--dx-project-name
	The name of the sequencing run project in DNAnexus.
--lane	The lane number of the flowcell on which the library was sequenced. This is added as a property to all projects in DNAnexus through the ‘seq_lane_index’ property. Use this in conjunction with –library-name and –uhts-run-name to further restrict the project search space.
-b, --barcode	The barcode of the sequenced sample. If specified, then only FASTQs with these barcodes will be downloaded. Otherwise, all FASTQs will be downloaded.
-d, --file-download-dir
	Local directory in which to download the FASTQ files.
--not-found-error
	Presence of this options means to raise an Exception if a project can’t be found on DNAnexus with the provided input. Default: False