add set -e -o pipefail to all relevant imputation tasks (#1434)

Co-authored-by: Jose Soto <[email protected]>

tasks/broad/ImputationTasks.wdl

@@ -12,6 +12,8 @@ task CalculateChromosomeLength {
   }
 
   command {
+    set -e -o pipefail
+
     grep -P "SN:~{chrom}\t" ~{ref_dict} | sed 's/.*LN://' | sed 's/\t.*//'
   }
   runtime {
@@ -38,6 +40,8 @@ task GetMissingContigList {
   }
 
   command <<<
+    set -e -o pipefail
+
     grep "@SQ" ~{ref_dict} | sed 's/.*SN://' | sed 's/\t.*//' > contigs.txt
     awk 'NR==FNR{arr[$0];next} !($0 in arr)' ~{included_contigs} contigs.txt > missing_contigs.txt
   >>>
@@ -543,7 +547,6 @@ task UpdateHeader {
   String disable_sequence_dict_validation_flag = if disable_sequence_dictionary_validation then "--disable-sequence-dictionary-validation" else ""
 
   command <<<
-
     ## update the header of the merged vcf
     gatk --java-options "-Xms~{command_mem}m -Xmx~{max_heap}m" \
     UpdateVCFSequenceDictionary \
@@ -644,6 +647,7 @@ task OptionalQCSites {
   Float hwe = select_first([optional_qc_hwe, 0.000001])
   command <<<
     set -e -o pipefail
+
     ln -sf ~{input_vcf} input.vcf.gz
     ln -sf ~{input_vcf_index} input.vcf.gz.tbi
 
@@ -676,6 +680,7 @@ task MergeSingleSampleVcfs {
   }
   command <<<
     set -e -o pipefail
+
     # Move the index file next to the vcf with the corresponding name
 
     declare -a VCFS=(~{sep=' ' input_vcfs})
@@ -715,6 +720,8 @@ task CountSamples {
   }
 
   command <<<
+    set -e -o pipefail
+
     bcftools query -l ~{vcf} | wc -l
   >>>
   runtime {
@@ -915,6 +922,7 @@ task SetIDs {
   }
   command <<<
     set -e -o pipefail
+
     bcftools annotate ~{vcf} --set-id '%CHROM\:%POS\:%REF\:%FIRST_ALT' -Oz -o ~{output_basename}.vcf.gz
     bcftools index -t ~{output_basename}.vcf.gz
   >>>
@@ -1074,6 +1082,8 @@ task FindSitesUniqueToFileTwoOnly {
     Int disk_size_gb = ceil(size(file1, "GiB") + 2*size(file2, "GiB")) + 10
   }
   command <<<
+    set -e -o pipefail
+
     comm -13 <(sort ~{file1} | uniq) <(sort ~{file2} | uniq) > missing_sites.ids
   >>>
   runtime {