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Changed count-collection tasks to use NIO for BAMs in CNV WDLs. #5015

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Changed count-collection tasks to use NIO for BAMs in CNV WDLs. #5015

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1682895
Changed count-collection tasks to use NIO for BAMs in CNV WDLs.
samuelklee Jul 16, 2018
7d7ba3d
Fixed entity_id type.
samuelklee Jul 16, 2018
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8 changes: 4 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 @@ -93,8 +93,8 @@ task AnnotateIntervals {

task CollectCounts {
File intervals
File bam
File bam_idx
String bam
String bam_idx
File ref_fasta
File ref_fasta_fai
File ref_fasta_dict
Expand Down Expand Up @@ -145,8 +145,8 @@ task CollectCounts {

task CollectAllelicCounts {
File common_sites
File bam
File bam_idx
String bam
String bam_idx
File ref_fasta
File ref_fasta_fai
File ref_fasta_dict
Expand Down
4 changes: 2 additions & 2 deletions scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl
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Expand Up @@ -419,7 +419,7 @@ workflow CNVSomaticPairWorkflow {
output {
File preprocessed_intervals = PreprocessIntervals.preprocessed_intervals

File read_counts_entity_id_tumor = CollectCountsTumor.entity_id
String read_counts_entity_id_tumor = CollectCountsTumor.entity_id
File read_counts_tumor = CollectCountsTumor.counts
File allelic_counts_entity_id_tumor = CollectAllelicCountsTumor.entity_id
File allelic_counts_tumor = CollectAllelicCountsTumor.allelic_counts
Expand All @@ -443,7 +443,7 @@ workflow CNVSomaticPairWorkflow {
File scaled_delta_MAD_tumor = PlotDenoisedCopyRatiosTumor.scaled_delta_MAD
File modeled_segments_plot_tumor = PlotModeledSegmentsTumor.modeled_segments_plot

File? read_counts_entity_id_normal = CollectCountsNormal.entity_id
String? read_counts_entity_id_normal = CollectCountsNormal.entity_id
File? read_counts_normal = CollectCountsNormal.counts
File? allelic_counts_entity_id_normal = CollectAllelicCountsNormal.entity_id
File? allelic_counts_normal = CollectAllelicCountsNormal.allelic_counts
Expand Down