Merge pull request #525 from moka-guys/develop

Develop (#525) Co-Authored-By: MokaGuys <mokaguys@gmail.com> Co-Authored-By: Aled Jones <aledjones@nhs.net> Co-Authored-By: RachelDuffin <rachel.g.duffin@gmail.com>
moka-guys · Dec 19, 2023 · 2d9b74a · 2d9b74a
2 parents 86c6e99 + 8744cee
commit 2d9b74a
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diff --git a/automate_demultiplex_config.py b/automate_demultiplex_config.py
@@ -277,20 +277,20 @@
 
 ### exome depth
 # exome depth readcount app
-ED_readcount_path = "Apps/ED_readcount_analysis_v1.2.0"
+ED_readcount_path = "Apps/ED_readcount_analysis_v1.3.0"
 ED_readcount_path_instance_type = "mem1_ssd1_v2_x8"
 #exome depth variant calling app
-ED_cnvcalling_path = "Apps/ED_cnv_calling_v1.2.0"
+ED_cnvcalling_path = "Apps/ED_cnv_calling_v1.3.0"
 ED_cnvcalling_instance_type = "mem1_ssd1_v2_x4"
 #VCP1 exome depth
-ED_readcount_normals_VCP1_file= "project-ByfFPz00jy1fk6PjpZ95F27J:file-GZYK6380f66PPy4kjzVQ7xj8"#"Pan5191_normals_v1.0.0.RData"
+ED_readcount_normals_VCP1_file= "project-ByfFPz00jy1fk6PjpZ95F27J:file-Gbv7Yb80v8Q40f8v140QBPQv"#"Pan5191_normals_v1.1.0.RData"
 ED_VCP1_readcount_BEDfile_pannum = "Pan5191_exomedepth.bed" 
 #VCP2 normals data file
-ED_readcount_normals_VCP2_file="project-ByfFPz00jy1fk6PjpZ95F27J:file-GZYbq400YG627Q12g1bbP440"#"Pan5188_normals_v1.0.0.RData"
+ED_readcount_normals_VCP2_file="project-ByfFPz00jy1fk6PjpZ95F27J:file-Gbkgyq00ZpxpFKx03zVPJ9GX"#"Pan5188_normals_v1.1.0.RData"
 ED_VCP2_readcount_BEDfile_pannum = "Pan5188_exomedepth.bed" 
 #VCP3 normals data file
-ED_readcount_normals_VCP3_file=None #"Pan5149_normals_v1.0.0.RData"
-ED_VCP3_readcount_BEDfile_pannum = None #"Pan5149_exomedepth.bed" 
+ED_readcount_normals_VCP3_file="project-ByfFPz00jy1fk6PjpZ95F27J:file-GbkY5v80jjgjkJqPXbgFpYzF"#"Pan5192_normals_v1.0.0.RData"
+ED_VCP3_readcount_BEDfile_pannum = "Pan5192_exomedepth.bed"
 
 exomedepth_refgenome_file = "project-ByfFPz00jy1fk6PjpZ95F27J:file-B6ZY7VG2J35Vfvpkj8y0KZ01" #hs37d5.fa.gz from 001
 ## readcount app inputs
@@ -981,7 +981,7 @@
         "sambamba_bedfile": "Pan5123dataSambamba.bed",
         "variant_calling_bedfile": "Pan5119data.bed",
         "polyedge": "MSH2",
-        "exome_depth_cnvcalling_BED": "Pan5193" # use R211 CNV bedfile
+        "exome_depth_cnvcalling_BED": "Pan5206"
     },
     "Pan4130": {  # VCP2 R211 polyposis (Viapath)
         "mokapipe": True,
@@ -1099,7 +1099,7 @@
         "hsmetrics_bedfile": "Pan4995data.bed",
         "sambamba_bedfile": "Pan4995dataSambamba.bed",
         "variant_calling_bedfile": "Pan4995data.bed",
-        # "exome_depth_cnvcalling_BED": "Pan5174" # CNV BED not yet available
+        "exome_depth_cnvcalling_BED": "Pan5174"
     },
     "Pan4144": {  # VCP3 R78 (Viapath)
         "mokapipe": True,
@@ -1120,7 +1120,7 @@
         "hsmetrics_bedfile": "Pan4995data.bed",
         "sambamba_bedfile": "Pan4995dataSambamba.bed",
         "variant_calling_bedfile": "Pan4995data.bed",
-        #"exome_depth_cnvcalling_BED": "Pan5168" #Exome depth does not support VCP3 yet
+        "exome_depth_cnvcalling_BED": "Pan5168"
     },
     "Pan4146": {  # VCP3 R81 CM (Viapath)
         "mokapipe": True,
@@ -1131,7 +1131,7 @@
         "hsmetrics_bedfile": "Pan4995data.bed",
         "sambamba_bedfile": "Pan4995dataSambamba.bed",
         "variant_calling_bedfile": "Pan4995data.bed",
-        #"exome_depth_cnvcalling_BED": "Pan5170" #Exome depth does not support VCP3 yet
+        "exome_depth_cnvcalling_BED": "Pan5170"
     },
     "Pan4151": {  # VCP3 R82 limb girdle (Viapath)
         "mokapipe": True,
@@ -1152,7 +1152,7 @@
         "hsmetrics_bedfile": "Pan4995data.bed",
         "sambamba_bedfile": "Pan4995dataSambamba.bed",
         "variant_calling_bedfile": "Pan4995data.bed",
-        #"exome_depth_cnvcalling_BED": "Pan5177" #Exome depth does not support VCP3 yet
+        "exome_depth_cnvcalling_BED": "Pan5177"
     },
     "Pan4387": {  # VCP3 R90 Bleeding and platelet disorders (Viapath)
         "mokapipe": True,
@@ -1163,7 +1163,7 @@
         "hsmetrics_bedfile": "Pan4995data.bed",
         "sambamba_bedfile": "Pan4995dataSambamba.bed",
         "variant_calling_bedfile": "Pan4995data.bed",
-        #"exome_depth_cnvcalling_BED": "Pan5171" #Exome depth does not support VCP3 yet
+        "exome_depth_cnvcalling_BED": "Pan5171" 
     },
     "Pan4390": {  # VCP3 R97 Thrombophilia with a likely monogenic cause (Viapath)
         "mokapipe": True,
@@ -1174,7 +1174,7 @@
         "hsmetrics_bedfile": "Pan4995data.bed",
         "sambamba_bedfile": "Pan4995dataSambamba.bed",
         "variant_calling_bedfile": "Pan4995data.bed",
-        #"exome_depth_cnvcalling_BED": "Pan5173",  #Exome depth does not support VCP3 yet
+        "exome_depth_cnvcalling_BED": "Pan5173",
     },
     "Pan4314": {  # VCP3 R229 (Viapath)
         "mokapipe": True,
@@ -1185,7 +1185,7 @@
         "hsmetrics_bedfile": "Pan4995data.bed",
         "sambamba_bedfile": "Pan4995dataSambamba.bed",
         "variant_calling_bedfile": "Pan4995data.bed",
-        # "exome_depth_cnvcalling_BED": "Pan5179", bedfile not yet made
+        "exome_depth_cnvcalling_BED": "Pan5179",
     },
     "Pan4396": {  # ArcherDx (Synnovis)
         "archerdx": True,
@@ -1376,7 +1376,7 @@
         "hsmetrics_bedfile": "Pan4995data.bed",
         "variant_calling_bedfile": "Pan4995data.bed",
         "sambamba_bedfile": "Pan4995dataSambamba.bed",
-        # "exome_depth_cnvcalling_BED": "Pan5174" BEDfile not yet available
+        "exome_depth_cnvcalling_BED": "Pan5174"
     },
     "Pan4832": {  # VCP3 STG R78
         "mokapipe": True,
@@ -1401,7 +1401,7 @@
         "hsmetrics_bedfile": "Pan4995data.bed",
         "variant_calling_bedfile": "Pan4995data.bed",
         "sambamba_bedfile": "Pan4995dataSambamba.bed",
-        # "exome_depth_cnvcalling_BED": "Pan5168", #Exome depth does not support VCP3 yet
+        "exome_depth_cnvcalling_BED": "Pan5168",
     },
     "Pan4834": {  # VCP3 STG R81
         "mokapipe": True,
@@ -1414,7 +1414,7 @@
         "hsmetrics_bedfile": "Pan4995data.bed",
         "variant_calling_bedfile": "Pan4995data.bed",
         "sambamba_bedfile": "Pan4995dataSambamba.bed",
-        #"exome_depth_cnvcalling_BED":  "Pan5170", #Exome depth does not support VCP3 yet
+        "exome_depth_cnvcalling_BED":  "Pan5170",
     },
     "Pan4835": {  # VCP3 STG R82
         "mokapipe": True,
@@ -1439,7 +1439,7 @@
         "hsmetrics_bedfile": "Pan4995data.bed",
         "variant_calling_bedfile": "Pan4995data.bed",
         "sambamba_bedfile": "Pan4995dataSambamba.bed",
-        #"exome_depth_cnvcalling_BED": "Pan5179" BEDfile not yet available
+        "exome_depth_cnvcalling_BED": "Pan5179"
     },
     "Pan4819": {  # VCP2 STG R210
         "mokapipe": True,
@@ -1453,7 +1453,7 @@
         "variant_calling_bedfile": "Pan5119data.bed",
         "sambamba_bedfile": "Pan5123dataSambamba.bed",
         "polyedge": "MSH2",
-        "exome_depth_cnvcalling_BED": "Pan5193" # useR211 bedfile
+        "exome_depth_cnvcalling_BED": "Pan5206"
     },
     "Pan4820": {  # VCP2 STG R211
         "mokapipe": True,

diff --git a/upload_and_setoff_workflows.py b/upload_and_setoff_workflows.py
@@ -1785,7 +1785,7 @@ def determine_exome_depth_requirements(self,pannnumber_list):
             # first build readcount command
             command_list.append(self.build_ED_readcount_cmd(set(VCP3), config.ED_readcount_normals_VCP3_file,config.ED_VCP3_readcount_BEDfile_pannum))
             command_list.append(self.add_to_depends_list("exomedepth", 'depends_list_ED_readcount'))
-            for panel in set(VCP2):# then build cnvcalling commands
+            for panel in set(VCP3):# then build cnvcalling commands
                 command_list.append(self.build_ED_cnv_calling_cmd(panel))
 
         return command_list