extract_multiqc

codescripts/extract_multiqc.py

@@ -50,6 +50,7 @@ dat =pd.DataFrame.from_records(happy)
 dat = dat.loc[:, dat.columns.str.endswith('ALL')]
 dat_transposed = dat.T
 benchmark = dat_transposed.loc[:,['sample_id','METRIC.Precision','METRIC.Recall']]
+benchmark['sample_id'] = benchmark.index
 benchmark.columns = ['Sample','Precision','Recall']
 
 #output

tasks/D5_D6.wdl

@@ -19,7 +19,7 @@
 				sample_j=$(echo $j | cut -f7 -d_)
 				rep_i=$(echo $i | cut -f8 -d_)
 				rep_j=$(echo $j | cut -f8 -d_)
-				if [[ $sample_i == "LCL5" ] && [ $sample_j == "LCL6" ] && [ $rep_i == $rep_j ]];then
+				if [ $sample_i == "LCL5" ] && [ $sample_j == "LCL6" ] && [ $rep_i == $rep_j ];then
 					cat $i | grep -v '##' | cut -f1,2,4,5,10 | cut -d ':' -f1 > LCL5.txt
 					cat $j | grep -v '##' | cut -f10 | cut -d ':' -f1 > LCL6.txt
 					paste LCL5.txt LCL6.txt > sister.txt