while read id; do ( acd $id && ( if [[ -e sentieon ]] && grep -q TNscope sentieon/log; then sname=$(id2sampleId "$PWD"); grep -oP 'COMMAND\s*\K.*' sentieon/log; echo 'rm sentieon/!(*bed)'; echo "rm -r sentieon scratch/sentieon preprocess; mkdir -p sentieon preprocess"; grep -oP 'COMMAND\s*\K.*' preprocess/log; fi ) | sed 's|/ref/|/devel/|g' | sed -E "s/(--tumor_sample ')[^']+/\1$sname/" | sed -E "s|'(\S+)/[0-9]*.bed'|\1/*.bed|" | perl -pe 's|\d+\.1\.vcf|sentieon/variants.tmp.vcf|; s|\d+\.2\.vcf|sentieon/variants.vcf|; END{print "bgzip sentieon/*vcf