Name all outputs with sample id

[fkollingiv]

We use the circuitseq pipeline to sequence plasmids at scale for customers and our platform for data delivery relies on files starting with "{SampleID}_". This works well for the final assembly where the sample id is added to the filename, but the intermediate files are only labelled by the barcode/well position. It would be great if the sample id was included in the file name for other outputs as well (bams in particular) so we could easily share these results with our users.