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bugfix for type of some output files in cnv_somatic_pair_workflow.wdl #6735

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merged 2 commits into from
Dec 14, 2022
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bugfix for type of some output files in cnv_somatic_pair_workflow.wdl #6735

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e21873a
bugfix for type of some output files
slzhao Aug 1, 2020
2e27f69
Merge branch 'master' of github.com:broadinstitute/gatk
slzhao Mar 14, 2021
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21 changes: 13 additions & 8 deletions scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -515,9 +515,9 @@ 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
String allelic_counts_entity_id_tumor = CollectAllelicCountsTumor.entity_id
File allelic_counts_tumor = CollectAllelicCountsTumor.allelic_counts
File denoised_copy_ratios_tumor = DenoiseReadCountsTumor.denoised_copy_ratios
File standardized_copy_ratios_tumor = DenoiseReadCountsTumor.standardized_copy_ratios
Expand Down Expand Up @@ -545,9 +545,9 @@ workflow CNVSomaticPairWorkflow {
Float scaled_delta_MAD_value_tumor = PlotDenoisedCopyRatiosTumor.scaled_delta_MAD_value
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
String? allelic_counts_entity_id_normal = CollectAllelicCountsNormal.entity_id
File? allelic_counts_normal = CollectAllelicCountsNormal.allelic_counts
File? denoised_copy_ratios_normal = DenoiseReadCountsNormal.denoised_copy_ratios
File? standardized_copy_ratios_normal = DenoiseReadCountsNormal.standardized_copy_ratios
Expand Down Expand Up @@ -575,10 +575,15 @@ workflow CNVSomaticPairWorkflow {
Float? scaled_delta_MAD_value_normal = PlotDenoisedCopyRatiosNormal.scaled_delta_MAD_value
File? modeled_segments_plot_normal = PlotModeledSegmentsNormal.modeled_segments_plot

File oncotated_called_file_tumor = select_first([CNVOncotatorWorkflow.oncotated_called_file, "null"])
File oncotated_called_gene_list_file_tumor = select_first([CNVOncotatorWorkflow.oncotated_called_gene_list_file, "null"])
File funcotated_called_file_tumor = select_first([CNVFuncotateSegmentsWorkflow.funcotated_seg_simple_tsv, "null"])
File funcotated_called_gene_list_file_tumor = select_first([CNVFuncotateSegmentsWorkflow.funcotated_gene_list_tsv, "null"])
# File? oncotated_called_file_tumor = select_first([CNVOncotatorWorkflow.oncotated_called_file, "null"])
# File? oncotated_called_gene_list_file_tumor = select_first([CNVOncotatorWorkflow.oncotated_called_gene_list_file, "null"])
# File? funcotated_called_file_tumor = select_first([CNVFuncotateSegmentsWorkflow.funcotated_seg_simple_tsv, "null"])
# File? funcotated_called_gene_list_file_tumor = select_first([CNVFuncotateSegmentsWorkflow.funcotated_gene_list_tsv, "null"])

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File? oncotated_called_file_tumor = CNVOncotatorWorkflow.oncotated_called_file
File? oncotated_called_gene_list_file_tumor = CNVOncotatorWorkflow.oncotated_called_gene_list_file
File? funcotated_called_file_tumor = CNVFuncotateSegmentsWorkflow.funcotated_seg_simple_tsv
File? funcotated_called_gene_list_file_tumor = CNVFuncotateSegmentsWorkflow.funcotated_gene_list_tsv
}
}

Expand Down