auto_process_ngs.commands.publish_qc_cmd

class auto_process_ngs.commands.publish_qc_cmd.PublishQCSchedulerReporter

Custom reporter for scheduler

auto_process_ngs.commands.publish_qc_cmd.publish_qc(ap, projects=None, location=None, ignore_missing_qc=False, regenerate_reports=False, force=False, use_hierarchy=False, exclude_zip_files=False, legacy=False, runner=None, base_url=None, suppress_warnings=False)

Copy the QC reports to the webserver

Looks for and copies various QC reports and outputs to a ‘QC server’ directory, and generates an HTML index.

The reports include:

  • processing QC reports

  • ‘cellranger mkfastq’ QC report

  • barcode analysis report

Also if the analysis includes project directories then for each Fastq set in each project:

  • QC report for standard QC

Also if a project comprises ICELL8 or 10xGenomics Chromium data:

  • ICELL8 processing reports, or

  • ‘cellranger count’ reports for each sample

In ‘legacy’ mode, the top-level report will also contain explicit links for each project for the following (where appropriate):

  • ICELL8 processing reports

  • cellranger count outputs

  • MultiQC report

(These reports should now be accessible from the per-project QC reports, regardless of whther ‘legacy’ mode is specified.)

Raises an exception if:

  • ‘source’ and ‘run_number’ metadata items are not set

  • a subset of projects don’t have associated QC outputs (unless ‘ignore_missing_qc’ is True)

Parameters:

  • ap (AutoProcessor) – autoprocessor pointing to the analysis directory to publish QC for

  • projects (str) – specify a glob-style pattern to match one or more projects to publish the reports for (default is to publish all reports)

  • location (str) – override the target location specified in the settings; can be of the form ‘[[user@]server:]directory’

  • ignore_missing_qc (bool) – if True then skip directories with missing QC data or reports (default is to raise an exception if projects have missing QC)

  • regenerate_reports (bool) – if True then try to create reports even when they already exist (default is to use existing reports)

  • force (bool) – if True then force QC report (re)generation even if QC is unverified (default is to raise an exception if projects cannot be verified)

  • use_hierarchy (bool) – if True then publish to a YEAR/PLATFORM subdirectory under the target location (default is not to use the hierarchy)

  • exclude_zip_files (bool) – if True then exclude any ZIP archives from publication (default is to include ZIP files)

  • legacy (bool) – if True then operate in ‘legacy’ mode (i.e. explicitly include MultiQC reports for each project)

  • runner (JobRunner) – explicitly specify the job runner to send jobs to (overrides runner set in the configuration)

  • base_url (str) – base URL for the QC server

  • suppress_warnings (bool) – if True then don’t report warnings in QC reports or the index page (even if there are missing metrics in individual reports)