Remove docker command wrappers; CPSR refactor

[pdiakumis]

• Cleaning up the codebase to get rid of the ('legacy') docker wrappers.
• Cleaned up the CPSR script in the process. Refactored its functions into the other files to fit with the PCGR modularisation.

Still got a bit of testing to do during the week so keeping this as a draft PR.

TODO:

• Remove the rm -f bits which scare me a bit. We can replace with os.remove().
• Test CPSR
• Test PCGR

[pdiakumis]

Okay, think this is ready for review whenever you're back on board @sigven.
Summary of changes:

• General changes:
  • use python f-strings throughout
  • apply 4-space indentation (instead of a mix of 3 and 2-space)
  • improve logging (a few things were getting duplicated in the logs since there were some loggers with the same name used).
• pcgr/main.py:
  • remove docker_uid and no_docker CLI args
  • simplify --maf_gnomad.. help msg
  • fix logging
  • remove docker stuff
• pcgr/cpsr.py:
  • move GE_panels to pcgr/pcgr_vars.py
  • fix indentation to 4 spaces
  • fix logging
  • add support for --version option
  • move check_args and verify_input_files to pcgr/arg_checker.py
• pcgr/pcgr_vars.py:
  • moved GE_panels here for displaying in CPSR help message.
• pcgr/utils.py:
  • removed docker-related stuff, added get_loftee_dir and get_cpsr_version funcs, moved is_integer func here.
• scripts/annoutils.py:
  • removed is_valid_vcf func since we've deprecated EBIvariation/vcf-validator
  • removed duplicated funcs to use those from pcgr/utils.py.
• scripts/pcgr_vcfanno.py:
  • mostly indentation, debug/logger refactor
• scripts/cpsr_validate_input.py and scripts/pcgr_validate_input.py:
  • use multiallelic_list list to track and display multiallelic variants in the log in a single list, instead of printing them all line by line. Example similar to the one below.
  • fix logger
• scripts/pcgr_summarise.py:
  • use funcs from pcgr/utils.py
  • better use of debug option
  • use vars_no_csq list to track and display variants with no VEP CSQ tag in the log in a single list, instead of printing them all line by line. Example:

Before:

2022-07-04 04:35:22 - pcgr-summarise - INFO - PCGR - STEP 3: Cancer gene annotations with pcgr-summarise
2022-07-04 04:35:22 - pcgr-summarise - INFO - pcgr_summarise.py /projects/sigverse/out/SBJ02242-somatic-PASS.pcgr_ready.vep.vcfanno.vcf.gz 0 0 /projects/sigverse/data/grch38 --debug
2022-07-04 04:35:22 - pcgr-gene-annotate - WARNING - Variant record g.1:7952954C>T has no CSQ tag from VEP (--vep_no_intergenic flag set?)  - skipping variant
2022-07-04 04:35:22 - pcgr-gene-annotate - WARNING - Variant record g.1:149040189C>T has no CSQ tag from VEP (--vep_no_intergenic flag set?)  - skipping variant
2022-07-04 04:35:22 - pcgr-gene-annotate - WARNING - Variant record g.1:164551593C>T has no CSQ tag from VEP (--vep_no_intergenic flag set?)  - skipping variant
2022-07-04 04:35:22 - pcgr-gene-annotate - WARNING - Variant record g.1:164859485A>T has no CSQ tag from VEP (--vep_no_intergenic flag set?)  - skipping variant
2022-07-04 04:35:22 - pcgr-gene-annotate - WARNING - Variant record g.1:164859486C>T has no CSQ tag from VEP (--vep_no_intergenic flag set?)  - skipping variant
[...]

After:

2022-07-04 05:07:13 - pcgr-gene-annotate - WARNING - The following 809 records do not have a CSQ tag from VEP (was --vep_no_intergenic flag set?) - skipping these variants:
----
g.1:7952954C>T, g.1:149040189C>T, g.1:164551593C>T, g.1:164859485A>T, g.1:164859486C>T, g.1:164860609C>T, g.1:164861170C>T, g.1:164866284G>A, [...]

• pcgr/arg_checker.py:
  • refactored two large CPSR functions and moved them to here
  • remove docker stuff
  • host_directories -> pcgr_paths