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)