make the dedup verification step resilient to http transient errors

Author: SHuang-Broad

wdl/tasks/Utility/BAMutils.wdl

@@ -721,6 +721,7 @@ task GetDuplicateReadnamesInQnameSortedBam {
     }
     input {
         File qns_bam
+        Boolean localize_bam = false
     }
 
     output {
@@ -729,40 +730,56 @@ task GetDuplicateReadnamesInQnameSortedBam {
     }
 
     command <<<
-        # the way this works is the following:
-        # 0) relying on the re-auth.sh script to export the credentials
-        # 1) perform the remote sam-view subsetting in the background
-        # 2) listen to the PID of the background process, while re-auth every 1200 seconds
+
         source /opt/re-auth.sh
         set -euxo pipefail
 
         # assumption
         sort_order=$(samtools view -H ~{qns_bam} | grep "^@HD" | tr '\t' '\n' | grep "^SO:" | awk -F ':' '{print $2}')
         if [[ "queryname" != "${sort_order}"  ]]; then echo -e "Sort order ${sort_oder} isn't the expected 'queryname'." && exit 1; fi
 
-        # remote grab read names
-        echo "false" > samtools.failed.txt
-        samtools view ~{qns_bam} \
-        | awk -F '\t' '{print $1}' \
-        | uniq -d  \
-        > "dup_read_names.txt" \
-        || { echo "true" > samtools.failed.txt; exit 77; } &
-        pid=$!
+        if ~{localize_bam}; then
+            time \
+            gcloud storage cp ~{qns_bam} name_does_not_matter.bam
 
-        set +e
-        count=1
-        while true; do
-            sleep 1200 && date && source /opt/re-auth.sh
-            if [[ ${count} -gt 2 ]]; then exit 0; fi
-            if ! pgrep -x -P $pid; then exit 0; fi
-            count=$(( count+1 ))
-        done
+            samtools view name_does_not_matter.bam \
+            | awk -F '\t' '{print $1}' \
+            | uniq -d  \
+            > "dup_read_names.txt"
+
+            echo "false" > samtools.failed.txt
+        else
+            # the way this works is the following:
+            # 0) relying on the re-auth.sh script to export the credentials
+            # 1) perform the remote sam-view operation in the background
+            # 2) listen to the PID of the background process, while re-auth every 1200 seconds
+
+            # remote grab read names
+            echo "false" > samtools.failed.txt
+            samtools view ~{qns_bam} \
+            | awk -F '\t' '{print $1}' \
+            | uniq -d  \
+            > "dup_read_names.txt" \
+            || { echo "true" > samtools.failed.txt; exit 77; } &
+            pid=$!
+
+            set +e
+            count=1
+            while true; do
+                sleep 1200 && date && source /opt/re-auth.sh
+                if [[ ${count} -gt 2 ]]; then exit 0; fi
+                if ! pgrep -x -P $pid; then exit 0; fi
+                count=$(( count+1 ))
+            done
+        fi
     >>>
 
+    Int disk_size = 5 + (if (localize_bam) then ceil(size(qns_bam, "Gib")) else 0)
+    String disk_type = if (localize_bam) then "SSD" else "HDD"
     runtime {
         cpu:            1
         memory:         "4 GiB"
-        disks:          "local-disk 10 HDD"
+        disks:          "local-disk ~{disk_size} ~{disk_type}"
         preemptible:    2
         maxRetries:     1
         docker: "us.gcr.io/broad-dsp-lrma/lr-gcloud-samtools:0.1.3"

wdl/tasks/Utility/ONTBamShardResetAndDeduplicate.wdl

@@ -22,8 +22,24 @@ workflow Work {
     call BU.SamtoolsReset as Magic { input: bam = shard_bam }
     call BU.QuerynameSortBamWithPicard as SortUnaligned { input: bam = Magic.res }
     call BU.DeduplicateQuerynameSortedBam as DeQS { input: qnorder_bam = SortUnaligned.qnsort_bam}
-    call BU.GetDuplicateReadnamesInQnameSortedBam as CheckDedupShard { input: qns_bam = DeQS.dedup_bam }
-    if ( CheckDedupShard.result_may_be_corrupted || 0!=length(read_lines(CheckDedupShard.dup_names_txt)) ) {
+
+    # verify
+    call BU.GetDuplicateReadnamesInQnameSortedBam as InitialCheckDedupShard { input: qns_bam = DeQS.dedup_bam }
+    if ( InitialCheckDedupShard.result_may_be_corrupted ) {
+        call BU.GetDuplicateReadnamesInQnameSortedBam as RetryCheckDedupShard { input: qns_bam = DeQS.dedup_bam }
+        if ( RetryCheckDedupShard.result_may_be_corrupted ) {
+            call BU.GetDuplicateReadnamesInQnameSortedBam as LastCheckDedupShard { input: qns_bam = DeQS.dedup_bam, localize_bam = true }
+        }
+    }
+
+    # do not change order
+    Boolean CheckOperationFailed = select_first([LastCheckDedupShard.result_may_be_corrupted,
+                                                 RetryCheckDedupShard.result_may_be_corrupted,
+                                                 InitialCheckDedupShard.result_may_be_corrupted])
+    Array[String] dup_names = read_lines(select_first([LastCheckDedupShard.dup_names_txt,
+                                                       RetryCheckDedupShard.dup_names_txt,
+                                                       InitialCheckDedupShard.dup_names_txt]))
+    if ( CheckOperationFailed || 0!=length(dup_names) ) {
         call Utils.StopWorkflow as DedupShardFail { input: reason = "Deduplication isn't successful for ~{shard_bam}."}
     }
 }