sample sheet filter script was patched in the current main branch to
handle passing through gtseq details, but this broke the GBS database import.
Workaround was to checkout earlier filter to get import done, then
discard that and restore back to main branch.
Need to change code so that two filtered sample sheets are generated: one goes
to the postprocesssing output folder and is used for GBS database import ; the
other remains in place in the sequencing output folder and has the extended fields
needed for general bcl2fastq including of non-GBS lanes.
afmcc
commented
5 years ago
sample sheet filter script was patched in the current main branch to handle passing through gtseq details, but this broke the GBS database import. Workaround was to checkout earlier filter to get import done, then discard that and restore back to main branch.
Need to change code so that two filtered sample sheets are generated: one goes to the postprocesssing output folder and is used for GBS database import ; the other remains in place in the sequencing output folder and has the extended fields needed for general bcl2fastq including of non-GBS lanes.