task quartet_mendelian { Array[File] project_mendelian_summary String project String docker String cluster_config String disk_size command <<< for i in ${sep=" " project_mendelian_summary} do cat $i | sed -n '2,3p' >> mendelian.summary done sed '1iFamily\tTotal_Variants\tMendelian_Concordant_Variants\tMendelian_Concordance_Rate' mendelian.summary > mendelian.txt cat mendelian.txt | grep 'INDEL' | cut -f4 | grep -v 'Mendelian_Concordance_Rate' | awk '{for(i=1;i<=NF;i++) {sum[i] += $i; sumsq[i] += ($i)^2}} END {for (i=1;i<=NF;i++) { printf "%f %f \n", sum[i]/NR, sqrt((sumsq[i]-sum[i]^2/NR)/NR)} }' >> quartet_indel_aver-std.txt cat mendelian.txt | grep 'SNV' | cut -f4 | grep -v 'Mendelian_Concordance_Rate' | awk '{for(i=1;i<=NF;i++) {sum[i] += $i; sumsq[i] += ($i)^2}} END {for (i=1;i<=NF;i++) { printf "%f %f \n", sum[i]/NR, sqrt((sumsq[i]-sum[i]^2/NR)/NR)} }' >> quartet_snv_aver-std.txt >>> runtime { docker:docker cluster:cluster_config systemDisk:"cloud_ssd 40" dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/" } output { File mendelian_summary="mendelian.txt" File snv_aver_std = "quartet_snv_aver-std.txt" File indel_aver_std = "quartet_indel_aver-std.txt" } }