Feature Counts Rule Enhancement

[Fred-White94]

It would be nice to add easy config option to determine feature level quantification of feature counts rule. As more frequently exon level analyses are getting popular in biomedical science. e.g.

config.yaml:

FEATURE: "exon_id"  #can be "exon_id" "transcript_id" "gene_id"

Snakefile:

rule create_counts_table:
        input:
            bams = expand(RESULT_DIR + "star/{sample}_Aligned.sortedByCoord.out.bam", sample = SAMPLES),
            gff  = config["refs"]["gtf"]
        output:
            WORKING_DIR + "raw_counts.tsv"
        message: "Producing the table of raw counts (counting read multimappers)"
        threads: 10
        shell:
            "featureCounts -T {threads} -M -t exon -g config["FEATURE"] -F 'gtf' -a {input.gff} -o {output} {input.bams}"

Perhaps with this modification the deseq MOR normalisation step should be disabled?