From 96d585f9e95c20c25c760ab7fd958674345b32f1 Mon Sep 17 00:00:00 2001
From: Emma Pierce-Hoffman <epierceh@broadinstitute.org>
Date: Sat, 27 Apr 2024 17:10:22 -0400
Subject: [PATCH] output id rename map

---
 wdl/ApplyNCRAndRefArtifactFilters.wdl          | 1 +
 wdl/ApplyNCRAndRefArtifactFiltersPerContig.wdl | 9 +++++++++
 2 files changed, 10 insertions(+)

diff --git a/wdl/ApplyNCRAndRefArtifactFilters.wdl b/wdl/ApplyNCRAndRefArtifactFilters.wdl
index 2a5ddf52b..b2cd62ea2 100644
--- a/wdl/ApplyNCRAndRefArtifactFilters.wdl
+++ b/wdl/ApplyNCRAndRefArtifactFilters.wdl
@@ -35,5 +35,6 @@ workflow ApplyNCRAndRefArtifactFilters {
   output {
     Array[File] filtered_vcfs = ApplyNCRAndRefArtifactFiltersPerContig.filtered_vcf
     Array[File] filtered_vcf_indexes = ApplyNCRAndRefArtifactFiltersPerContig.filtered_vcf_index
+    Array[File] id_rename_maps = ApplyNCRAndRefArtifactFiltersPerContig.id_rename_map
   }
 }
\ No newline at end of file
diff --git a/wdl/ApplyNCRAndRefArtifactFiltersPerContig.wdl b/wdl/ApplyNCRAndRefArtifactFiltersPerContig.wdl
index 48bc79d25..f7b8aa752 100644
--- a/wdl/ApplyNCRAndRefArtifactFiltersPerContig.wdl
+++ b/wdl/ApplyNCRAndRefArtifactFiltersPerContig.wdl
@@ -61,9 +61,17 @@ workflow ApplyNCRAndRefArtifactFiltersPerContig {
       runtime_attr_override = runtime_attr_concat_vcfs
   }
 
+  call tasks.CatUncompressedFiles {
+    input:
+      shards=ApplyFilters.id_rename_map,
+      outfile_name="~{prefix}.id_rename_map.tsv",
+      sv_base_mini_docker=sv_base_mini_docker
+  }
+
   output {
     File filtered_vcf = ConcatVcfs.concat_vcf
     File filtered_vcf_index = ConcatVcfs.concat_vcf_idx
+    File id_rename_map = CatUncompressedFiles.outfile
   }
 }
 
@@ -110,6 +118,7 @@ task ApplyFilters {
 
   output {
     File filtered_vcf = "~{prefix}.vcf.gz"
+    File id_rename_map = "~{cohort_id}.vid_map.tsv"
   }
 
   runtime {