From 1682895866b0692383570c741ea0889ded4c5414 Mon Sep 17 00:00:00 2001 From: Samuel Lee Date: Mon, 16 Jul 2018 10:59:23 -0400 Subject: [PATCH 1/2] Changed count-collection tasks to use NIO for BAMs in CNV WDLs. --- scripts/cnv_wdl/cnv_common_tasks.wdl | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/scripts/cnv_wdl/cnv_common_tasks.wdl b/scripts/cnv_wdl/cnv_common_tasks.wdl index eb9ce570aee..46a24568738 100755 --- a/scripts/cnv_wdl/cnv_common_tasks.wdl +++ b/scripts/cnv_wdl/cnv_common_tasks.wdl @@ -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 @@ -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 From 7d7ba3db30ac6c98675dfe12c65ad536b7893b2e Mon Sep 17 00:00:00 2001 From: Samuel Lee Date: Mon, 16 Jul 2018 11:45:01 -0400 Subject: [PATCH 2/2] Fixed entity_id type. --- scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl b/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl index 480bed70bf8..cb04c35eab7 100644 --- a/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl +++ b/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl @@ -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 @@ -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