Pipeline: split samples after demultiplexing but before aligning

[okartal]

See the GATK recommendations for preprocessing to properly mark duplicates and avoid secondary alignments:

• https://software.broadinstitute.org/gatk/documentation/article?id=6483
• https://software.broadinstitute.org/gatk/documentation/article?id=11020

also see https://www.biostars.org/p/256448/ to remove secondary alignments if necessary

[okartal]

DONE: Adressed by commit 7999529