Write equivalent sequence_align_and_tag.cwl for umi duplex and umi molecular pipelines.

[Sam16711]

Issue in reference to #935 . In order to support bam/fastq input for the umi duplex and umi molecular pipelines, an equivalent to sequence_align_and_tag.cwl will have to be written. Currently, both pipelines require fastq files that are eventually converted to bams using ../tools/fastq_to_bam.cwl.