Move R code away from snakemake files

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.

bihealth / seasnap-pipeline

Move R code away from snakemake files #6