Overall functionality

[Gregor Sturm]

The new pipeline should (at least) provide the functionality described in the docstring of the old script:

runDESeq2_ICBI.R
Usage:
  runDESeq2_ICBI.R <sample_sheet> <count_table> --result_dir=<res_dir> --c1=<c1> --c2=<c2> [options]
  runDESeq2_ICBI.R --help
Arguments:
  <sample_sheet>                CSV file with the sample annotations.
  <count_table>                 TSV file with the read counts
Mandatory options:
  --result_dir=<res_dir>        Output directory
  --c1=<c1>                     Contrast level 1 (perturbation). Needs to be contained in condition_col.
  --c2=<c2>                     Contrast level 2 (baseline). Needs to be contained in condition_col.
Optional options:
  --nfcore                      Indicate that the input samplesheet is from the nf-core RNA-seq ppipeline.
                                Will merge entries from the same sample and infer the sample_id from `group` and `replicate`.
                                If set, this option overrides `sample_col`.
  --condition_col=<cond_col>    Column in sample annotation that contains the condition [default: group]
  --sample_col=<sample_col>     Column in sample annotation that contains the sample names
                                (needs to match the colnames of the count table). [default: sample]
  --paired_grp=<paired_grp>     Column that conatins the name of the paired samples, when dealing with
                                paired data.
  --covariate_formula=<formula> Formula to model additional covariates (need to be columns in the samplesheet)
                                that will be appended to the formula built from `condition_col`.
                                E.g. `+ age + sex`. Per default, no covariates are modelled.
  --plot_title=<title>          Title shown above plots. Is built from contrast per default.
  --prefix=<prefix>             Results file prefix. Is built from contrasts per default.
  --fdr_cutoff=<fdr>            False discovery rate for GO analysis and volcano plots [default: 0.1]
  --fc_cutoff=<log2 fc cutoff>  Fold change (log2) cutoff for volcano plots [default: 1]
  --gtf_file=<gtf>              Path to the GTF file used for featurecounts. If specified, a Biotype QC
                                will be performed.
  --gene_id_type=<id_type>      Type of the identifier in the `gene_id` column compatible with AnnotationDbi [default: ENSEMBL]
  --n_cpus=<n_cpus>             Number of cores to use for DESeq2 [default: 1]
  --skip_gsea                   Skip Gene-Set-Enrichment-Analysis step
  --genes_of_interest=<genes>   File containing a list of genes to highlight in the volcano plot

See the project board for sub-tasks!