assembly strategy rationale implemented as suggested in
    http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html

    run Cufflinks in without a reference GTF for each individual sample
    merge the assemblies with Cuffmerge using a reference GTF

def assemble_transcripts(run_parallel, samples):
    """
    assembly strategy rationale implemented as suggested in
    http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html

    run Cufflinks in without a reference GTF for each individual sample
    merge the assemblies with Cuffmerge using a reference GTF
    """
    assembler = dd.get_in_samples(samples, dd.get_transcript_assembler)
    data = samples[0][0]
    if assembler:
        if "cufflinks" in assembler:
            samples = run_parallel("cufflinks_assemble", samples)
        if "stringtie" in assembler:
            samples = run_parallel("run_stringtie_expression", samples)
        if "stringtie" in assembler and stringtie.supports_merge(data):
            samples = run_parallel("stringtie_merge", [samples])
        else:
            samples = run_parallel("cufflinks_merge", [samples])
    return samples