Pipeline Cleanup #4
Description
Description of the bug
- Separate environment for genotype variants
- MSI file doesn't have results for the research samples
- Separate intermediate and final results directories
- One file for all CNA outputs
- infer_maf_paths function should not be in infer_bam_paths script
- maf file template should be in the nextflow config
- sample categories: assay_type "impact" "access", research_clinical "reseach", "clinical"
- missing categories? access research normals, access clinical simplex
- access clinical: unfilter.bam and standard.bam are not the same
- NA's in the filtering step
- ensure errors are thrown if genotyping fails (all 0s)
- check for required columns in the maf and type checks
- simply the config file with nested parameters for repeated dirs
- no need to specify bai paths separately
Command used and terminal output
Relevant files
No response
System information
No response