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upload_runfolder script

Uploads an Illumina runfolder to DNAnexus.

Protocol

  1. Searches DNAnexus for the project given as an input. If the input is 'None', searches for a project matching self.rf_obj.runfolder_name
  2. If upload_rest_of_runfolder is called, calls methods to upload the rest of the runfolder (the runfolder minus the fastqs and several QC files):
    • Checks the runfolder exists
    • Creates a dictionary of all files and folders requiring upload, ignoring any files specified in the ignore string. Folders are the keys and files in the folders are values in list format
    • Builds upload commands to upload the rest of the runfolder using the DNAnexus ua utility. The number of upload tries is set to 100 with the --tries flag. The upload agent itself can take multiple files separated by a space, with the full path required for each file, and it has a max number of uploads of 1000 per command. The function in the script generates per-folder upload commands, with a maximum of 100 files uploaded per command
    • Orthogonal tests are performed to verify the upload:
      • A count of files that should be uploaded (using the ignore terms if provided)
      • A count of files in the DNA Nexus project
      • (If relevant) A count of files in the DNA Nexus project containing a pattern to be ignored. NB this may not be accurate if the ignore term is found in the result of dx find data (eg present in project name)
    • Counts the number of files to be uploaded and checks if any were uploaded to DNAnexus that should have been ignored
  3. If upload_files is called directly, uploads the provided files to the runfolder
  4. The script uploads logfiles produced by this repository to the DNAnexus project under PROJECT:/RUNFOLDER/automated_scripts_logfiles.
  • N.B. the script does not upload the SampleSheet from the SampleSheets directory, unless it has been copied into the runfolder first *

Configuration

Settings are imported from ad_config.py.

Usage

This tool requires the DNAnexus utilities ua (upload agent) and dx (DNAnexus toolkit) to be available in the system PATH. Python3 is required, and this tool uses packages from the standard library.

The script can be either imported as a module, or run directly from the command line.

Command line

usage: Upload user-specified runfolder to DNAnexus, providing an auth token, project ID to upload to, and any file patterns that should be ignored

Uploads runfolder to DNAnexus

options:
  -h, --help            show this help message and exit
  -r RUNFOLDER_NAME, --runfolder_name RUNFOLDER_NAME
                        Workstation runfolder name
  --ignore IGNORE       Comma-separated list of patterns which prevents the file from being uploaded if any pattern is present in filename or filepath.
  -p PROJECT_ID, --project_id PROJECT_ID
                        The ID of an existing DNAnexus project for the given runfolder

Module import

When run as a module import, the above inputs are supplied in the following format:

N.B. nexus_identifiers is an optional input - if not supplied, the script will search for the matching project in DNAnexus using the runfolder name

# Dictionary containing DNAnexus project name and id
nexus_identifiers = {
    "proj_name": project_name,
    "proj_id": project_id,
    }

self.upload_runfolder = UploadRunfolder(
    rf_obj.rf_loggers["backup"],
    rf_obj.runfolder_name,
    rf_obj.runfolderpath,
    rf_obj.upload_flagfile,
    nexus_identifiers
)

result = self.upload_runfolder.upload_files(
    file_upload_dict[filetype]["cmd"],
    file_upload_dict[filetype]["files_list"],
)

ignore = "DNANexus_upload_started,add_runfolder_to_nexus_cmds"

self.upload_runfolder.upload_rest_of_runfolder(ignore)

Logging

Alias Description Filename Location
backup Records the logs from the upload runfolder script RUNFOLDERNAME_upload_runfolder.log /usr/local/src/mokaguys/automate_demultiplexing_logfiles/upload_runfolder_script_logfiles/
upload_agent Records upload agent logs (stdout and stderr of the upload agent) DNANexus_upload_started.txt Within the runfolder

Testing

N.B. Tests and test cases/files MUST be maintained and updated accordingly in conjunction with script development

This script does not yet have a test suite.