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config.yaml
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config.yaml
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### Note: To keep the suggested file and directory structure run "snakemake dir_setup"
### This will generate a subfolder structure as presented here within your directory.
### It will only work if an 'out' and a 'log' folder already exist
## general settings
ROOT: "."
R_lib: "renv/library/"
src: "src/"
log: "logs/"
out: "out/"
## Path to scripts
src_data: "src/datasets/"
src_meta: "src/meta_files/"
src_data_mgt: "src/data_management/"
src_analysis: "src/analysis/"
src_com: "src/comparison/"
src_summary: "src/summary_files/"
src_de: "src/de_files/"
src_index: "src/index_files/"
src_metric: "src/metric_files/"
src_fig: "src/figure_files/"
src_plot: "src/figures/"
src_norm: "src/normalization/"
src_time_dat: "src/time_data/"
src_time: "src/time/"
## Path to output
out_time: "out/time/"
out_cms_def: "out/cms_default/"
out_cms_kmin: "out/cms_kmin/"
out_cms_bmin: "out/cms_bmin/"
out_mm: "out/mm/"
out_wisi: "out/wisi/"
out_isi: "out/isi/"
out_entr: "out/entropy/"
out_lisi: "out/lisi/"
out_asw: "out/asw/"
out_kbet: "out/kbet/"
out_pcr: "out/pcr/"
out_gcon: "out/graph_connectivity/"
out_cor: "out/cor_summary/"
out_res: "out/res/"
out_fig_obj: "out/res/fig_objects/"
out_fig: "out/res/figs/"
out_norm: "out/normalization/"
out_time_dat: "out/time_data/"
out_time_res: "out/time_res/"
out_bench: "out/benchmark/"
## Path to logs
log_dir: "log/dir_setup/"
log_cms_def: "log/cms_default/"
log_cms_kmin: "log/cms_kmin/"
log_cms_bmin: "log/cms_bmin/"
log_mm: "log/mm/"
log_wisi: "log/wisi/"
log_isi: "log/isi/"
log_entr: "log/entropy/"
log_lisi: "log/lisi/"
log_asw: "log/asw/"
log_kbet: "log/kbet/"
log_pcr: "log/pcr/"
log_gcon: "log/graph_connectivity/"
log_norm: "log/normalization/"
log_time: "log/time/"
## Path to website files
docs: "docs/"
docs_libs: "docs/site_libs"
## Subdirectory names
### Names of subfdirectories to be generated in output and log directories
### Here they correspond to the rule names
dir_names: time cms_default cms_kmin cms_bmin mm isi wisi entropy lisi kbet asw pcr gcon out_cor out_res time time_dat