[NF] Reorganize out directory

[jylee-bcm]

Currently ${outdir} directory is organized like this

${outdir}/
├── phrank
│   └── ${run_id}.phrank.txt
├── prediction
│   └── conf_4Model
│       ├── ${run_id}_default_predictions.csv
│       ├── ${run_id}_nd_predictions.csv
│       ├── ${run_id}_nd_recessive_predictions.csv
│       ├── ${run_id}_recessive_predictions.csv
│       └── integrated
│           └── ${run_id}_integrated.csv
├── reference_index
│   ├── final_hg19.dict
│   ├── final_hg19.fa
│   └── final_hg19.fa.fai
├── vcf
│   ├── ${run_id}.filt.rmBL.vcf
│   ├── ${run_id}.filt.rmMT.vcf.gz
│   └── ${run_id}.filt.rmMT.vcf.gz.tbi
└── vep
    └── ${run_id}-vep.txt

But the problem is that some directories might not be related to ${run_id}, (e.g. reference_index) so I would like to suggest like that:

${out_dir}/
    ${run_id}/
        phrank/
        prediction/
        vcf/
        vep/
    general/
        reference_index/

Secondarily, I would like to suggest several data dependency files to be constructed in the nextflow pipeline,and stored under the ${out_dir}/general/ for previously generated and stored in the aim_data_dependencies of mod5_diffusion/net_norm_cor_GeneID.npz, etc. .

Tasks

• [x] Use run id inside outdir
• [ ] #85
• [ ] Use storeDir to generate exome_filter