Containers, parameters, general to-do

Next steps:

[ ] change hairpin process to run within singularity image (shub://MathijsSanders/SangerLCMFilteringSingularity)
[ ] build singularity image for vcf_flag_modifier.py (python packages - pkg_resources, argparse, os, sys) (based on docker://quay.io/wtsicgp/vcf_flag_modifier)
[ ] add parameter to set project_type (whole genome / whole exome)
[ ] try to set default image to null for all processes and then specify containers for containerised processes afterwards (like in https://github.com/alextidd/chemo_trees/blob/main/nf-chemo-trees/nextflow.config)
[ ] figure out why phuong branch is hidden
[ ] set defaults for fragment length filtering: CLPM = 0, ASRD = 1 (can set 0.87), ASMD = 140 - create a parameter. If ASRD is passed, ASMD filter is skipped. ASRD always supercedes ASMD.
[ ] parameterise all of the arguments
[x] nf-schema for the parameters

Potential future steps:

[ ] change from cgpVAF to bamtoR based method (ask Andrew and Pan), or parallelise cgpVAF by chromosome + batch up by patient (10 samples per job, same bed intervals per patient) (@alextidd)
[ ] Add parameters to switch between clone tree and sample tree?
[ ] conpair

Phuong-Le / process_sanger_lcm-nf