2.4.1-2

• Minor: Changed comparison-operator in checkSampleSwap_TiN.pl to allow for + signs in PID names.
• Minor: Adding local control AF annotations from WES cohort via deepAnnotation pipe. The WGS local control annotation is already available in the 2.4.1 version. These annotations will be used for the reduced coverage filters in the downstream workflows.
• Patch: Add exit-code tests on Perl-backtick invocations.

Consistent PDF generation in corner cases & No exit != 0 if few germline variants

• Now no exit code != 0 is raised if there are less than 50 germline variants in the tinda job.
• If less than 50 germline variants are found, now an PDF with a warning message is produced
• The germline-variant count was off by one (1 to much). This is fixed.
• If there are zero germline variants now a PDF with a warning message is produced.

selectSampleExtractionMethod "version_2"

• Update to COWorkflowsBasePlugin 1.4.1 that supports the selectSampleExtractionMethod:version_2 for better handling of sample names with underscores in them.
• Check readability of reference genome upon submission and in jobs (via COWorkflowsBasePlugin).