From c66bbbd4f9e7e56ca15d8644e506abc0d742c340 Mon Sep 17 00:00:00 2001
From: Samuel Lee <lee.samuel.k@gmail.com>
Date: Fri, 15 Feb 2019 08:59:23 -0500
Subject: [PATCH] Cleaned up intermediate files in gCNV WDL. (#5382)

---
 scripts/cnv_wdl/cnv_common_tasks.wdl                  | 11 ++++++-----
 .../cnv_wdl/germline/cnv_germline_case_workflow.wdl   |  9 ++++++---
 .../cnv_wdl/germline/cnv_germline_cohort_workflow.wdl |  8 +++++---
 3 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/scripts/cnv_wdl/cnv_common_tasks.wdl b/scripts/cnv_wdl/cnv_common_tasks.wdl
index a46a0391981..1519ab112ce 100644
--- a/scripts/cnv_wdl/cnv_common_tasks.wdl
+++ b/scripts/cnv_wdl/cnv_common_tasks.wdl
@@ -405,21 +405,22 @@ task PostprocessGermlineCNVCalls {
             model_args="$model_args --model-shard-path MODEL_$index"
         done
 
-        mkdir extracted-contig-ploidy-calls
-        tar xzf ${contig_ploidy_calls_tar} -C extracted-contig-ploidy-calls
+        mkdir contig-ploidy-calls
+        tar xzf ${contig_ploidy_calls_tar} -C contig-ploidy-calls
 
         gatk --java-options "-Xmx${command_mem_mb}m" PostprocessGermlineCNVCalls \
             $calls_args \
             $model_args \
             ${sep=" " allosomal_contigs_args} \
             --autosomal-ref-copy-number ${ref_copy_number_autosomal_contigs} \
-            --contig-ploidy-calls extracted-contig-ploidy-calls \
+            --contig-ploidy-calls contig-ploidy-calls \
             --sample-index ${sample_index} \
             --output-genotyped-intervals ${genotyped_intervals_vcf_filename} \
             --output-genotyped-segments ${genotyped_segments_vcf_filename}
 
-        rm -r CALLS_*
-        rm -r MODEL_*
+        rm -rf CALLS_*
+        rm -rf MODEL_*
+        rm -rf contig-ploidy-calls
     >>>
 
     runtime {
diff --git a/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl b/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl
index 11717fbfb4e..aa8d7242180 100644
--- a/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl
+++ b/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl
@@ -372,8 +372,8 @@ task GermlineCNVCallerCaseMode {
         export MKL_NUM_THREADS=${default=8 cpu}
         export OMP_NUM_THREADS=${default=8 cpu}
 
-        mkdir contig-ploidy-calls-dir
-        tar xzf ${contig_ploidy_calls_tar} -C contig-ploidy-calls-dir
+        mkdir contig-ploidy-calls
+        tar xzf ${contig_ploidy_calls_tar} -C contig-ploidy-calls
 
         mkdir gcnv-model
         tar xzf ${gcnv_model_tar} -C gcnv-model
@@ -381,7 +381,7 @@ task GermlineCNVCallerCaseMode {
         gatk --java-options "-Xmx${command_mem_mb}m"  GermlineCNVCaller \
             --run-mode CASE \
             --input ${sep=" --input " read_count_files} \
-            --contig-ploidy-calls contig-ploidy-calls-dir \
+            --contig-ploidy-calls contig-ploidy-calls \
             --model gcnv-model \
             --output ${output_dir_} \
             --output-prefix case \
@@ -425,6 +425,9 @@ task GermlineCNVCallerCaseMode {
             tar czf case-gcnv-calls-shard-${scatter_index}-sample-$CURRENT_SAMPLE_WITH_LEADING_ZEROS.tar.gz -C ${output_dir_}/case-calls/SAMPLE_$CURRENT_SAMPLE .
             let CURRENT_SAMPLE=CURRENT_SAMPLE+1
         done
+
+        rm -rf contig-ploidy-calls
+        rm -rf gcnv-model
     >>>
 
     runtime {
diff --git a/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl b/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl
index bebb4999637..450eaa27ae5 100644
--- a/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl
+++ b/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl
@@ -487,14 +487,14 @@ task GermlineCNVCallerCohortMode {
         export MKL_NUM_THREADS=${default=8 cpu}
         export OMP_NUM_THREADS=${default=8 cpu}
 
-        mkdir contig-ploidy-calls-dir
-        tar xzf ${contig_ploidy_calls_tar} -C contig-ploidy-calls-dir
+        mkdir contig-ploidy-calls
+        tar xzf ${contig_ploidy_calls_tar} -C contig-ploidy-calls
 
         gatk --java-options "-Xmx${command_mem_mb}m"  GermlineCNVCaller \
             --run-mode COHORT \
             -L ${intervals} \
             --input ${sep=" --input " read_count_files} \
-            --contig-ploidy-calls contig-ploidy-calls-dir \
+            --contig-ploidy-calls contig-ploidy-calls \
             ${"--annotated-intervals " + annotated_intervals} \
             --interval-merging-rule OVERLAPPING_ONLY \
             --output ${output_dir_} \
@@ -549,6 +549,8 @@ task GermlineCNVCallerCohortMode {
             tar czf ${cohort_entity_id}-gcnv-calls-shard-${scatter_index}-sample-$CURRENT_SAMPLE_WITH_LEADING_ZEROS.tar.gz -C ${output_dir_}/${cohort_entity_id}-calls/SAMPLE_$CURRENT_SAMPLE .
             let CURRENT_SAMPLE=CURRENT_SAMPLE+1
         done
+
+        rm -rf contig-ploidy-calls
     >>>
 
     runtime {