v2.0.1

Summary

This is a minor bug fix update to improve:

• finding clinical indications and panels against test codes
• correctly add multiple clinical indications to a list for a sample when present on multiple lines in the Gemini input file (manifest or reanalysis tsv)
• name panel-specific bed files with test_code only to avoid hitting the filesystem character limit, especially at the eggd_annotate_excluded_regions stage of the dias_cnvreports_workflow.

Changes

parse_Gemini_manifest:

• restrict parsing of clinical indications that start with an R code, C code or _HGNC ID
• correctly identify ALL test codes for a sample that may be across multiple lines within the reanalysis file

create_job_report_file:

• present list of samples and invalid test codes as one pair per line for easier copy-pasting to repeat analysis job with corrected test codes

in the reports.py and cnvreports.py:

• match only on the R code part of the clinical indication from a Gemini file to genepanels
• provide a && joined string of test codes as optional input to all generate_bed stages (output_file_prefix input field)

Bug fixes:

#78
#101

For further information including development notes and testing evidence, see: https://cuhbioinformatics.atlassian.net/wiki/spaces/DV/pages/2888663263/dias+batch+running+v2.0.1