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fix: gcnv contig wrapper scripts do not clean their output folders (#443)#468

Merged
Nicolai-vKuegelgen merged 6 commits intomainfrom 443-gcnv_contig_ploidy-wrapper-script-crahses-because-gatk-determinegermlinecontigploidy-output-is-not-cleaned-but-always-fully-readNov 29, 2023