rna seq workflow for use with qproject.

Add a config file "params.json" in etc:

{
    "gtf": "path/to/gtf",
    "indexed_genome": "path/to/genome/basename",
    "stranded": "no",
    "overlap_mode": "union",
    "feature_type": "exon",
    "gff_attribute": "gene_id",
    "normalize_counts": "deseq2"
}

where indexed_genome and gtf are paths relative to ref.

indexed_genome is the basename of a bowtie2 index.

The parameters stranded, overlap_mode, feature_type and gff_attribute are explained in the htseq documentation.