From 79f60f537da1a7088713fcbf75bc3fd78dbd1ab4 Mon Sep 17 00:00:00 2001 From: Adetunji Date: Tue, 11 Jun 2024 09:28:28 -0500 Subject: [PATCH] SE annotation in output files --- peaseq-case.wdl | 4 ++++ peaseq-control.wdl | 4 ++++ seaseq-case.wdl | 2 ++ seaseq-control.wdl | 2 ++ workflows/tasks/rose.wdl | 2 ++ 5 files changed, 14 insertions(+) diff --git a/peaseq-case.wdl b/peaseq-case.wdl index 78b1cbe..e49790e 100755 --- 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 index 16e6560..969733c 100755 --- 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 index 3619aeb..c902edb 100755 --- 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 index d45f1f8..f5a1eb7 100755 --- 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 index 6f4b0a9..294ed06 100755 --- 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" } }