SE annotation in output files

stjude · Jun 11, 2024 · 79f60f5 · 79f60f5
1 parent d29ba17
commit 79f60f5
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Showing 5 changed files with 14 additions and 0 deletions.
diff --git a/peaseq-case.wdl b/peaseq-case.wdl
@@ -1198,6 +1198,8 @@ workflow peaseq {
         File? g_to_e_enhancers = SE_rose.g_to_e_enhancers
         File? e_to_g_super_enhancers = SE_rose.e_to_g_super_enhancers
         File? g_to_e_super_enhancers = SE_rose.g_to_e_super_enhancers
+        File? supergenes = SE_rose.super_genes
+        File? allgenes = SE_rose.all_genes
         File? sp_pngfile = PE_rose.pngfile
         File? sp_mapped_union = PE_rose.mapped_union
         File? sp_mapped_stitch = PE_rose.mapped_stitch
@@ -1211,6 +1213,8 @@ workflow peaseq {
         File? sp_g_to_e_enhancers = PE_rose.g_to_e_enhancers
         File? sp_e_to_g_super_enhancers = PE_rose.e_to_g_super_enhancers
         File? sp_g_to_e_super_enhancers = PE_rose.g_to_e_super_enhancers
+        File? sp_supergenes = PE_rose.super_genes
+        File? sp_allgenes = PE_rose.all_genes
 
         #MOTIFS
         File? flankbedfile = SE_flankbed.flankbedfile

diff --git a/peaseq-control.wdl b/peaseq-control.wdl
@@ -2009,6 +2009,8 @@ workflow peaseq {
         File? g_to_e_enhancers = SE_rose.g_to_e_enhancers
         File? e_to_g_super_enhancers = SE_rose.e_to_g_super_enhancers
         File? g_to_e_super_enhancers = SE_rose.g_to_e_super_enhancers
+        File? supergenes = SE_rose.super_genes
+        File? allgenes = SE_rose.all_genes
         File? sp_pngfile = PE_rose.pngfile
         File? sp_mapped_union = PE_rose.mapped_union
         File? sp_mapped_stitch = PE_rose.mapped_stitch
@@ -2022,6 +2024,8 @@ workflow peaseq {
         File? sp_g_to_e_enhancers = PE_rose.g_to_e_enhancers
         File? sp_e_to_g_super_enhancers = PE_rose.e_to_g_super_enhancers
         File? sp_g_to_e_super_enhancers = PE_rose.g_to_e_super_enhancers
+        File? sp_supergenes = PE_rose.super_genes
+        File? sp_allgenes = PE_rose.all_genes
 
         #MOTIFS
         File? flankbedfile = SE_flankbed.flankbedfile

diff --git a/seaseq-case.wdl b/seaseq-case.wdl
@@ -737,6 +737,8 @@ workflow seaseq {
         File? g_to_e_enhancers = rose.g_to_e_enhancers
         File? e_to_g_super_enhancers = rose.e_to_g_super_enhancers
         File? g_to_e_super_enhancers = rose.g_to_e_super_enhancers
+        File? supergenes = rose.super_genes
+        File? allgenes = rose.all_genes
 
         #MOTIFS
         File? flankbedfile = flankbed.flankbedfile

diff --git a/seaseq-control.wdl b/seaseq-control.wdl
@@ -1228,6 +1228,8 @@ workflow seaseq {
         File? g_to_e_enhancers = rose.g_to_e_enhancers
         File? e_to_g_super_enhancers = rose.e_to_g_super_enhancers
         File? g_to_e_super_enhancers = rose.g_to_e_super_enhancers
+        File? supergenes = rose.super_genes
+        File? allgenes = rose.all_genes
 
         #MOTIFS
         File? flankbedfile = flankbed.flankbedfile

diff --git a/workflows/tasks/rose.wdl b/workflows/tasks/rose.wdl
@@ -167,5 +167,7 @@ task rose {
         File? g_to_e_enhancers = "~{default_location}/unionpeaks_AllStitched_GENE_TO_REGION.txt"
         File? e_to_g_super_enhancers = "~{default_location}/unionpeaks_SuperStitched_REGION_TO_GENE.txt"
         File? g_to_e_super_enhancers = "~{default_location}/unionpeaks_SuperStitched_GENE_TO_REGION.txt"
+        File? super_genes = "~{default_location}/unionpeaks_SuperStitched.table_withGENES.txt"
+        File? all_genes = "~{default_location}/unionpeaks_AllStitched.table_withGENES.txt"
     }
 }