Making QC reports available using `auto_process publish_qc`

Overview

Once QC reports have been generated from run_qc they can be copied to a webserver or other location using the publish_qc command.

If a QC server has been specified in the configuration file then the reports can be published there using

auto_process.py publish_qc

If no server was configured (or to copy to an alternative destination) use the --qc_dir option, for example:

auto_process.py publish_qc --qc_dir=/mnt/qc_reports

Note

The destination specified by --qc_dir can be either a local or a remote directory; to specify a remote destination, use the [USER@]HOST:DIR syntax.

If a base URL is also specified (either in the configuration, or via the --url option) then the URL of the published HTML index will also be reported.

Repeated runs of publish_qc will update the copies on the server.

Using a hierarchy for publication

By default the QC will be copied to a directory with the same name as the analysis directory, directly underneath the target directory - for example:

/mnt/qc_reports/180817_M00123_0001_000000000-BV1X2_analysis

However this can quickly lead to an extremely cluttered QC server directory if reports are not removed periodically.

To mitigate this, specifying --use-hierarchy=yes inserts two additional directory levels to the final destination, to create a YEAR/PLATFORM hierarchy. For the previous example this would result in something like:

/mnt/qc_reports/2018/miseq/180817_M00123_0001_000000000-BV1X2_analysis

Selecting subsets of projects for publication

By default the QC for all the projects in the analysis directory will be copied; to only publish the QC for a subset, specify their names using the --projects option.

Handling projects with failed QC

Reports will only be published if the QC is verified for all the specified projects associated with the run; otherwise the publish command will stop.

However there are a number of options available to handle this situation:

Use the --ignore-missing-qc to only publish projects which pass the verification, skipping those with missing QC, or
Specify the --force command to ignore the failed QC and force generation and publication of the missing QC.

For #2, the reports for the projects with failed QC will contain a warning message in the header, and the links to the reports will be marked with a warning icon in the index page. The --suppress-warnings options can be used along with --force to suppress these warnings if necessary.

Note

--suppress-warnings will only suppress warnings in new QC reports; to make this option apply to all reports, combine it with the --regenerate-reports option.

Updating QC reports on publication

Sometimes it is useful to regenerate the QC reports for all projects, in which case the --regenerate-reports option can be specified to force all the reports to be regenerated prior to publication.

Making QC reports available using auto_process publish_qc