updated the af plot output structure

broadinstitute · Apr 29, 2024 · 7f2129f · 7f2129f
1 parent 4c142f5
commit 7f2129f
Showing 1 changed file with 11 additions and 11 deletions.
diff --git a/BenchmarkCNV/Clinical_CNV_Eval/Clinical_CNV_Eval.wdl b/BenchmarkCNV/Clinical_CNV_Eval/Clinical_CNV_Eval.wdl
@@ -149,6 +149,8 @@ CODE
             String Wittyer_Postprocess_Docker = "us.gcr.io/tag-team-160914/cnv-clinical-eval:0.1.1-alpha"
             File Proband_ShortVariant_VCF
             File Normal_ShortVariant_VCF
+            Int memory = 16
+            Int cpu = 4
         }
         command <<<
     set -e
@@ -168,17 +170,18 @@ CODE
                 mv *_compare_sv.png wittyer_comparison_plot.png
             fi
 
-            # Rename the truth LOH status file
-            mv truth_*_LOH.png truth_heterozyogisty_status.png
-            mv *_short_variants_stats.csv short_variants_within_truth_interval_stats.csv
+            # Rename the truth ROH status file
+            mv *_AF_plots.png proband_vs_normal_af_plot.png
+
 
 
     >>>
         runtime {
             docker: Wittyer_Postprocess_Docker
             preemptible: 2
-            memory: "32 GB"
-            cpu: "4"
+            memory: memory + " GB"
+            cpu: cpu
+            disks: "local-disk 100 HDD"
         }
         output {
             Int truth_length = read_int("truth_length.txt")
@@ -188,12 +191,9 @@ CODE
             String merged_eval_decision = read_string("merged_eval_decision.txt")
             String merged_overlap_ratio = read_string("merged_overlap_ratio.txt")
             File? comparison_plot = "wittyer_comparison_plot.png"
-            File short_variants_within_truth_interval_stats = "short_variants_within_truth_interval_stats.csv"
-            File heterozyogisty_within_truth_interval_plot = "truth_heterozyogisty_status.png"
-            Float proband_hom_percentage = read_float("proband_hom_percentage.txt")
-            Float proband_het_percentage = read_float("proband_het_percentage.txt")
-            Float normal_hom_percentage = read_float("normal_hom_percentage.txt")
-            Float normal_het_percentage = read_float("normal_het_percentage.txt")
+            File proband_snp_af_within_truth_interval_stats = "proband_snp_within_interval_af.csv"
+            File normal_snp_af_within_truth_interval_stats = "normal_snp_within_interval_af.csv"
+            File heterozyogisty_within_truth_interval_plot = "proband_vs_normal_af_plot.png"
         }
     }