Move R code away from snakemake files

[eudesbarbosa]

Issue
R code is kept in the Snakemake files and directly take variables from it. For example, rule filter in DE_pipeline. Snakemake:

rule filter:
	""" filter experiment & genes before normalisation, based on counts and/or GTF property"""
	input:
		...
	run:
		config_file = pph.file_path(step="pipeline_report", extension="yaml", contrast="all")
		script = textwrap.dedent(r"""
		#----- import packages
		library(DESeq2)
		library(AnnotationDbi)

		{R_SESSION_INFO}

		conf.f   <- "{config_file}"

		#----- load config
		config <- yaml::yaml.load_file(conf.f)

		#----- read counts in dds format
		dds <- readRDS("{input.rds}")
		sample_df <- as.data.frame(SummarizedExperiment::colData(dds))
		rownames(sample_df) <- as.character(sample_df$label)
		...

Possible solution
Isolate all R code on specific files, the location can be accessed via config, for instance. Structure the code in a way that is possible to pass the Snakemake variables as arguments (silly example). Once the code is isolated it should be easier to stablish unit tests for all of them.