BREAKING CHANGES Add pileup step in the pipeline#111
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FerriolCalvet merged 6 commits intomainfrom Jun 21, 2024
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- update test csv file to 4 columns - input processing scripts - update altdepth selection in modules.config - update mutated epithelium to include running and using recomputed pileup pending: - update test to work with AM - update dynamic definition of ALT_DEPTH category according to provided bam + parameter
- remove older input formats - adjust resources for sample panel and annotate depths modules
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Add step to run pileup within the pipeline.