Define VAF distortion threshold from the nextflow.config

[FerriolCalvet]

This threshold is the one that we should be able to provide from the nextflow.config

deepCSA/bin/vcf2maf.py

Lines 209 to 229 in 1612083

	dat_full["VAF_AM"] = dat_full["ALT_DEPTH_AM"] / dat_full["DEPTH_AM"]
	dat_full["VAF_distortion"] = dat_full["VAF_AM"] / dat_full["VAF"]
	dat_full["VAF_distorted_expanded"] = dat_full["VAF_distortion"] > 3
	dat_full["VAF_distorted_reduced"] = (1 / dat_full["VAF_distortion"]) > 3
	dat_full["VAF_distorted_expanded"] = dat_full["VAF_distorted_expanded"].fillna(True)
	dat_full["VAF_distorted_reduced"] = dat_full["VAF_distorted_reduced"].fillna(True)
	dat_full["VAF_distorted"] = dat_full["VAF_distorted_reduced"] | dat_full["VAF_distorted_expanded"]
	dat_full["ALT_DEPTH_ND"] = dat_full["ALT_DEPTH_AM"] - dat_full["ALT_DEPTH"]
	dat_full["DEPTH_ND"] = dat_full["DEPTH_AM"] - dat_full["DEPTH"]
	dat_full["VAF_ND"] = dat_full["ALT_DEPTH_ND"] / dat_full["DEPTH_ND"]
	else:
	dat_full["VAF_distortion"] = 1
	dat_full["VAF_distorted"] = False
	dat_full["VAF_distorted_reduced"] = False
	dat_full["VAF_distorted_expanded"] = False