postprocessing.lsf

#BSUB -W 240:00
#BSUB -q e80long
#BSUB -n 70
#BSUB -M 800
#BSUB -R rusage[mem=800]
#BSUB -o /rsrch5/home/genetics/NAVIN_LAB/Ryan/projects/metact/250526_RMMM_scalebio_dcis/%J_postprocessing.log
#BSUB -cwd /rsrch5/home/genetics/NAVIN_LAB/Ryan/projects/metact/250526_RMMM_scalebio_dcis
#BSUB -u RMulqueen@mdanderson.org
#BSUB -J 250526_RMMM_scalebio_dcis

#load modules
module load nextflow/23.04.3

#set up environment variables
export SCRATCH="/rsrch4/scratch/genetics/rmulqueen"
export projDir="/rsrch5/home/genetics/NAVIN_LAB/Ryan/projects/metact"
export srcDir="/rsrch5/home/genetics/NAVIN_LAB/Ryan/projects/metact/src"
export refDir="/rsrch5/home/genetics/NAVIN_LAB/Ryan/projects/metact/ref"

#set directory
mkdir -p ./metatlas_nextflow
cd ./metatlas_nextflow

#call nextflow
nextflow ${srcDir}/singlecell_met_nf.groovy \
--refdir $refDir \
-w ${SCRATCH}/met_work \
--scalemethylout ${projDir}/250526_RMMM_scalebio_dcis \
--cnv_call "TRUE" \
-resume