No singularity

This is an experiment done without singularity during the analysis of WGS (so no WES here, either) data.

SLURM scripts

#!/usr/bin/bash

#SBATCH --job-name=_rva
#SBATCH --account=CARDIO-SL0-CPU
#SBATCH --partition=cardio
#SBATCH --cpus-per-task=9
#SBATCH --qos=cardio
#SBATCH --array=1-368
#SBATCH --mem=28800
#SBATCH --time=5-00:00:00
#SBATCH --output=/rds/user/jhz22/hpc-work/work/_rva_%A_%a.o
#SBATCH --error=/rds/user/jhz22/hpc-work/work/_rva_%A_%a.e
#SBATCH --export ALL

export TMPDIR=${HPC_WORK}/work
export SEQ=~/COVID-19/SCALLOP-Seq
export COHORT=INTERVAL

no_singularity_exec()
{
  if [ ! -d ${SEQ}/rva/${weswgs}-${pheno} ]; then mkdir -p ${SEQ}/rva/${weswgs}-${pheno}; fi
  Rscript ${SEQ}/burden_testing/step2 --cohort-name ${COHORT} \
                                      --GDS ${SEQ}/work/${weswgs}-${chr}.gds \
                                      --group-file ${SEQ}/${group_file} \
                                      --matrix-prefix ${SEQ}/work/${weswgs} \
                                      --matrix-type GCTA \
                                      --pheno ${SEQ}/work/${weswgs}/${pheno}-lr.pheno \
                                      --out ${SEQ}/rva/${weswgs}-${pheno}/${COHORT}-${weswgs}-${pheno}-${group}-${chr} \
                                      --threads 9
}

export groups=(exon_CADD exon_reg exon_severe reg_Only)
for weswgs in wgs
do
  export pheno=$(ls ${SEQ}/work/${weswgs}/*-lr.pheno | xargs -I {} basename {} -lr.pheno | awk 'NR==ENVIRON["SLURM_ARRAY_TASK_ID"]')
  export weswgs=${weswgs}
  for chrs in {1..22}
  do
    export chr=chr${chrs}
    for group in ${groups[@]}
    do
      export group_file=${group}-${chrs}.groupfile.txt
      echo ${pheno} ${weswgs} ${chr} ${group}
      no_singularity_exec
    done
  done
done