crg.cleanup.pbs

#!/bin/bash
#PBS -l walltime=0:5:00,nodes=1:ppn=1
#PBS -joe .
#PBS -d .
#PBS -l vmem=4g,mem=4g


#this script is for cleaning up a completed crg run prior to moving
#results to /hpf/largeprojects/ccm_dccforge/dccdipg/c4r_wgs/results/
#usage: qsub crg_cleanup.pbs -F <family>
#run from within top level of crg directory

FAMILY=$1

#move bams and multiqc to top level directory
mv bcbio-align/${FAMILY}/final/${FAMILY}_*/*bam* .
mv bcbio-small-variants/${FAMILY}/multiqc .

#remove unecessary folders
rm -r  bcbio-align/${FAMILY}/final/  bcbio-align/${FAMILY}/work/ bcbio-align/${FAMILY}/input/
rm -r  bcbio-small-variants/${FAMILY}/sv/
rm -r remove_decoys

#cleanup bcbio-sv directory
rm bcbio-sv/${FAMILY}*/${FAMILY}/final/${FAMILY}_*/*bam*
rm -r bcbio-sv/${FAMILY}*/${FAMILY}/work
rm -r bcbio-sv/${FAMILY}*/${FAMILY}/final/${FAMILY}_*/qc
rm -r bcbio-sv/svscoretmp bcbio-sv/*crg* bcbio-sv/snpEff_genes.txt bcbio-sv/snpEff_summary.html bcbio-sv/conf.toml

#cleanup genes directory
rm genes/*missing* genes/*unsorted*