remove cmake version

Update README.md with warning that creating conda environments when running the workflow for the first time may take some time.

Update workflow execution section of README.md (Snakemake requires the --cores parameter to be specified).

fix format

See merge request fonda_a6/popins2_snake!5

modify readme.md

See merge request fonda_a6/popins2_snake!4

integrate notebooks in workflow, define parameters in config file, fix dependencies

See merge request fonda_a6/popins2_snake!3

Update example_data/S0001/S0001.bam, example_data/S0001/S0001.bam.bai, example_data/S0002/S0002.bam, example_data/S0002/S0002.bam.bai, example_data/S0003/S0003.bam, example_data/S0003/S0003.bam.bai, example_data/virus_ref/altref_virus_clean.fa, example_data/virus_ref/altref_virus_clean.fa.amb, example_data/virus_ref/altref_virus_clean.fa.ann, example_data/virus_ref/altref_virus_clean.fa.bwt, example_data/virus_ref/altref_virus_clean.fa.pac, example_data/virus_ref/altref_virus_clean.fa.sa, example_data/chr21_ins.fa, example_data/chr21_ins.fa.fai
Deleted notebooks/.ipynb_checkpoints/contig_coverage_assessment_120721-checkpoint.ipynb, notebooks/.ipynb_checkpoints/unmapped_data_assessment_102121-checkpoint.ipynb, notebooks/src/__pycache__/__init__.cpython-38.pyc, notebooks/src/stat_func/__init__.py, notebooks/src/stat_func/calculator.py, notebooks/src/stat_func/visualization.py, notebooks/analyze_all_samples_110221.ipynb, notebooks/contig_coverage_assessment_120721.ipynb, notebooks/remapping_choice_032222.ipynb, notebooks/unmapped_data_assessment_102121.ipynb

workflow version control

See merge request fonda_a6/popins2_snake!2