Step 3: refminus for SE data

[isaacovercast]

Apparently reference_as_filter is not implemented in step 3 for single-end data. From clustmap.py:360 -

                # TODO: add support for refminus, needs testing still...
                # if self.data.params.reference_as_filter:
                #     # map reads to altref to get unmapped fastQ outputs
                #     # i: tmpdir/{}_R[1,2]-tmp.fa
                #     # o: tmpdir/{}-tmp-umap[1,2].FASTQ
                #     self.remote_run(
                #         function=mapping_reads,
                #         printstr=("mapping minus reads ", "s3"),
                #         args=(self.nthreads, 0,),
                #         threaded=True,
                #     )

Probably should actually implement this.