Latest pipeline versions fail to create aggregations foreach LN.

[rsandstromUW]

interestingly, aggregations have not been getting created for recent NCTE ALT-seq Librarypool internal libraries. The altseq-pipeline actually functions without them and produces valid results that can be used in downstream analysis. However it will not generate any results from the aggregation endpoint, meaning that a portion of metadata is silently missing (which is a responsibility of the altseq-pipeline to handle, of course).

I haven't looked into exactly what is failing, but i think it is in run_bcl2fastq_2.sh when the cluster specific alignment/aggregation steps are handled.

[rsandstromUW]

As i think about this, perhaps this is "as intended" and really what needs to happen is that there needs to be a clean up some altseq branch mde that removes spurious references to aggregation_identifiers, etc.