[NGL-Bi] add NGSRG treatment for element biosciences
linked with https://forgemia.inra.fr/get-plage/ngl-bi_client/-/issues/109
currently, there is a NGSRG process for illumina. We have to implement NGSRG at readsets level.
For lanes and run, it can be called within extractReads.sh, where NGL-Bi run creation will be done, after demux step
currently, we use perl the following command line for readsets :
createNGL-BiTreatmentNGSRG.pl \
--objectFile /aviti/analyzed/20241016_AV242804_SideB_REPDEV_run_ITCOM88_8pM/ReadsetsNGL-Bi.created \
--pathdemuxRunStatsFile /work/project/PlaGe/test/dev_AVITI/data/20241016_AV242804_SideB_REPDEV_run_ITCOM88_8pM_1729594238/RunStats.json \
--pathdemuxRunParametersFile /work/project/PlaGe/test/dev_AVITI/data/20241016_AV242804_SideB_REPDEV_run_ITCOM88_8pM_1729594238/RunParameters.json \
--laneNumberToWorkOn 1 \
--level readsets
Edited by Jules Sabban