Polishing scripts

[mariacuria]

• Use the utils module to navigate to config.json in scripts that use config.json
• Replace hardcoded paths with config.json paths
• Move processing scripts to convert_step2/cbioportal
• Add which script goes after which in README.md

[mariacuria]

@Reeya123
Scripts that need to use utils (some of them are bash scripts, so a separate bash utils would need to be created):

1. Everything in /data/shared/repos/biomuta-old/pipeline/download_step1/cbioportal
2. Everything in /data/shared/repos/biomuta-old/pipeline/convert_step2/cbioportal
3. In /data/shared/repos/biomuta-old/pipeline/convert_step2/liftover:
   1. 1_chr_pos_to_bed.py
   2. 2_liftover.sh

You might encounter some wrongly defined paths due to me changing the repo file tree. DM me if you stumble upon them.

[mariacuria]

How I store data:

1. Source data is supposed to be downloaded every month. It goes to /data/shared/biomuta/downloads/cbioportal/<yyyy_mm_dd> where <yyyy_mm_dd> is download date.
2. Data generated by scripts goes to /data/shared/biomuta/generated/datasets/<yyyy_mm_dd> where the date is not necessarily the same as in (1) but I expect it to be the same in most cases.

The logic I use to navigate to these file paths is to pull the main directories (downloads and datasets) from config.json, and then finding the latest subdirectory. Scripts that follow this logic:

• bash: /data/shared/repos/biomuta-old/pipeline/download_step1/cbioportal/cancer_types.sh
• python: /data/shared/repos/biomuta-old/pipeline/convert_step2/cbioportal/1_generate_cancer_do_json.py

[Reeya123]

Hello Maria. Please approve my pull request and merge with the main branch