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Fixed gCNV WDL broken by Cromwell update on FireCloud. #5407

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Merged
merged 1 commit into from
Nov 26, 2018
Merged

Fixed gCNV WDL broken by Cromwell update on FireCloud. #5407

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7 changes: 3 additions & 4 deletions scripts/cnv_wdl/cnv_common_tasks.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -340,7 +340,8 @@ task PostprocessGermlineCNVCalls {

String genotyped_intervals_vcf_filename = "genotyped-intervals-${entity_id}.vcf.gz"
String genotyped_segments_vcf_filename = "genotyped-segments-${entity_id}.vcf.gz"
Boolean allosomal_contigs_specified = defined(allosomal_contigs) && length(select_first([allosomal_contigs, []])) > 0

Array[String] allosomal_contigs_args = if defined(allosomal_contigs) then prefix("--allosomal-contig ", select_first([allosomal_contigs])) else []

String dollar = "$" #WDL workaround for using array[@], see https://github.com/broadinstitute/cromwell/issues/1819

Expand Down Expand Up @@ -371,12 +372,10 @@ task PostprocessGermlineCNVCalls {
mkdir extracted-contig-ploidy-calls
tar xzf ${contig_ploidy_calls_tar} -C extracted-contig-ploidy-calls

allosomal_contigs_args="--allosomal-contig ${sep=" --allosomal-contig " allosomal_contigs}"

gatk --java-options "-Xmx${command_mem_mb}m" PostprocessGermlineCNVCalls \
$calls_args \
$model_args \
${true="$allosomal_contigs_args" false="" allosomal_contigs_specified} \
${sep=" " allosomal_contigs_args} \
--autosomal-ref-copy-number ${ref_copy_number_autosomal_contigs} \
--contig-ploidy-calls extracted-contig-ploidy-calls \
--sample-index ${sample_index} \
Expand Down