Write equivalent sequence_align_and_tag.cwl for rnaseq, rnaseq_star_fusion, and rnaseq_star_fursion_xenosplit pipelines.

[Sam16711]

Issue in reference to #935 (making all pipelines compatibel with fastq or bams). In order to support bam/fastq input for the rna seq pipelines, an equivalent to sequence_align_and_tag.cwl will have to be written. Maybe a single cwl can be written to convert if the inputs are bams and if not, then continue to trimming? Currently, the pipelines require bams that are eventually converted to fastq and then trimmed.