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Fix an edge case for high scatter count in Mutect2 WDL #6216

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Oct 17, 2019
Merged

Fix an edge case for high scatter count in Mutect2 WDL #6216

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24 changes: 15 additions & 9 deletions scripts/mutect2_wdl/mutect2.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -275,8 +275,6 @@ workflow Mutect2 {

Int merged_vcf_size = ceil(size(M2.unfiltered_vcf, "GB"))
Int merged_bamout_size = ceil(size(M2.output_bamOut, "GB"))
Int merged_tumor_pileups_size = ceil(size(M2.tumor_pileups, "GB"))
Int merged_normal_pileups_size = ceil(size(M2.tumor_pileups, "GB"))

if (run_ob_filter) {
call LearnReadOrientationModel {
Expand Down Expand Up @@ -314,7 +312,7 @@ workflow Mutect2 {
if (defined(variants_for_contamination)) {
call MergePileupSummaries as MergeTumorPileups {
input:
input_tables = M2.tumor_pileups,
input_tables = flatten(M2.tumor_pileups),
output_name = output_basename,
ref_dict = ref_dict,
runtime_params = standard_runtime
Expand All @@ -323,7 +321,7 @@ workflow Mutect2 {
if (defined(normal_bam)){
call MergePileupSummaries as MergeNormalPileups {
input:
input_tables = M2.normal_pileups,
input_tables = flatten(M2.normal_pileups),
output_name = output_basename,
ref_dict = ref_dict,
runtime_params = standard_runtime
Expand Down Expand Up @@ -596,10 +594,15 @@ task M2 {
~{true='--f1r2-tar-gz f1r2.tar.gz' false='' run_ob_filter} \
~{m2_extra_args}

m2_exit_code=$?

### GetPileupSummaries
# These must be created, even if they remain empty, as cromwell doesn't support optional output
touch tumor-pileups.table
touch normal-pileups.table

# If the variants for contamination and the intervals for this scatter don't intersect, GetPileupSummaries
# throws an error. However, there is nothing wrong with an empty intersection for our purposes; it simply doesn't
# contribute to the merged pileup summaries that we create downstream. We implement this by with array outputs.
# If the tool errors, no table is created and the glob yields an empty array.
set +e

if [[ ! -z "~{variants_for_contamination}" ]]; then
gatk --java-options "-Xmx~{command_mem}m" GetPileupSummaries -R ~{ref_fasta} -I ~{tumor_bam} ~{"--interval-set-rule INTERSECTION -L " + intervals} \
Expand All @@ -610,6 +613,9 @@ task M2 {
-V ~{variants_for_contamination} -L ~{variants_for_contamination} -O normal-pileups.table
fi
fi

# the script only fails if Mutect2 itself fails
exit $m2_exit_code
>>>

runtime {
Expand All @@ -630,8 +636,8 @@ task M2 {
String normal_sample = read_string("normal_name.txt")
File stats = "~{output_stats}"
File f1r2_counts = "f1r2.tar.gz"
File tumor_pileups = "tumor-pileups.table"
File normal_pileups = "normal-pileups.table"
Array[File] tumor_pileups = glob("*tumor-pileups.table")
Array[File] normal_pileups = glob("*normal-pileups.table")
}
}

Expand Down