Merge pull request #448 from moka-guys/v44.3.6

update bed file for vcp3 - fix #442 (#448)
moka-guys · Nov 9, 2022 · 18f2796 · 18f2796
2 parents 713d75a + fe76e0f
commit 18f2796
Showing 1 changed file with 79 additions and 79 deletions.
diff --git a/automate_demultiplex_config.py b/automate_demultiplex_config.py
@@ -42,7 +42,7 @@
 # directories to be ignored when looping through runfolders
 ignore_directories = ["samplesheets", "GlacierTest"]
 
-demultiplex_test_folder = ["999999_M02353_0496_000000000-D8M36_demux_nointegrity","999999_A01229_0010_AHY5TWDRXX_demux_integrity","999999_A01229_0038_AH5MG7DRXY_TSO500","folder123","123_folder","999999_A01229_0049_AHMKGHDRXY_TSO500"]
+demultiplex_test_folder = ["999999_M02353_0496_000000000-DEMUX","999999_A01229_0010_DEMUXINTEG","999999_A01229_0049_AHMKTSO500"]
 
 # path to log file which records the output of the upload agent
 upload_and_setoff_workflow_logfile = (
@@ -603,9 +603,9 @@
 		"congenica_credentials": "STG",
 		"congenica_IR_template":"non-priority",
 		"congenica_project": "4201",
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
 	},
 	"Pan4119": {  #VCP1 R134_Familial hypercholesterolaemia-Familial hypercholesterolaemia Small panel (Viapath)
 	    "mokapipe": True,
@@ -834,139 +834,139 @@
 		"RPKM_bedfile_pan_number": "Pan4362",
 		"congenica_project": "5092",
 		"RPKM_also_analyse": vcp3_panel_list,
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
 	},
 	"Pan4134": {  #VCP3 R57 (Viapath)
 		"mokapipe": True,
 		"multiqc_coverage_level": 30,
 		"RPKM_bedfile_pan_number": "Pan4362",
 		"congenica_project": "5092",
 		"RPKM_also_analyse": vcp3_panel_list,
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
-		"variant_calling_bedfile": "Pan4535data.bed"
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
+		"variant_calling_bedfile": "Pan4995data.bed"
 	},
 	"Pan4136": {  #VCP3 R58 (Viapath)
 		"mokapipe": True,
 		"multiqc_coverage_level": 30,
 		"RPKM_bedfile_pan_number": "Pan4362",
 		"congenica_project": "5092",
 		"RPKM_also_analyse": vcp3_panel_list,
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
 	},
 	"Pan4137": {  #VCP3 R60 (Viapath)
 		"mokapipe": True,
 		"multiqc_coverage_level": 30,
 		"RPKM_bedfile_pan_number": "Pan4362",
 		"congenica_project": "5092",
 		"RPKM_also_analyse": vcp3_panel_list,
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
 	},
 	"Pan4138": {  #VCP3 R62 (Viapath)
 		"mokapipe": True,
 		"multiqc_coverage_level": 30,
 		"RPKM_bedfile_pan_number": "Pan4362",
 		"congenica_project": "5092",
 		"RPKM_also_analyse": vcp3_panel_list,
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
 	},
 	"Pan4143": {  #VCP3 R66 (Viapath)
 		"mokapipe": True,
 		"multiqc_coverage_level": 30,
 		"RPKM_bedfile_pan_number": "Pan4362",
 		"congenica_project": "5092",
 		"RPKM_also_analyse": vcp3_panel_list,
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
 	},
 	"Pan4144": {  #VCP3 R78 (Viapath)
 		"mokapipe": True,
 		"multiqc_coverage_level": 30,
 		"RPKM_bedfile_pan_number": "Pan4362",
 		"congenica_project": "5092",
 		"RPKM_also_analyse": vcp3_panel_list,
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
 	},
 	"Pan4145": {  #VCP3 R79 - CMD (Viapath)
 		"mokapipe": True,
 		"multiqc_coverage_level": 30,
 		"RPKM_bedfile_pan_number": "Pan4362",
 		"congenica_project": "4666",
 		"RPKM_also_analyse": vcp3_panel_list,
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
 	},
 	"Pan4146": {  #VCP3 R81 CM (Viapath)
 		"mokapipe": True,
 		"multiqc_coverage_level": 30,
 		"RPKM_bedfile_pan_number": "Pan4362",
 		"congenica_project": "4666",
 		"RPKM_also_analyse": vcp3_panel_list,
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
 	},
 	"Pan4151": {  #VCP3 R82 limb girdle (Viapath)
 		"mokapipe": True,
 		"multiqc_coverage_level": 30,
 		"RPKM_bedfile_pan_number": "Pan4362",
 		"congenica_project": "5092",
 		"RPKM_also_analyse": vcp3_panel_list,
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
 	},
 	"Pan4351": { #VCP3 R227 (Viapath)
 		"mokapipe": True,
 		"multiqc_coverage_level": 30,
 		"RPKM_bedfile_pan_number": "Pan4362",
 		"congenica_project": "5522",
 		"RPKM_also_analyse": vcp3_panel_list,
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
 	},
 	"Pan4387": { #VCP3 R90 Bleeding and platelet disorders (Viapath)
 		"mokapipe": True,
 		"multiqc_coverage_level": 30,
 		"RPKM_bedfile_pan_number": "Pan4362",
 		"congenica_project": "4699",
 		"RPKM_also_analyse": vcp3_panel_list,
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
 	},
 	"Pan4390": { #VCP3 R97 Thrombophilia with a likely monogenic cause (Viapath)
 		"mokapipe": True,
 		"multiqc_coverage_level": 30,
 		"RPKM_bedfile_pan_number": "Pan4362",
 		"congenica_project": "4699",
 		"RPKM_also_analyse": vcp3_panel_list,
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
 	},
 	"Pan4314": { #VCP3 R229 (Viapath)
 		"mokapipe": True,
 		"multiqc_coverage_level": 30,
 		"RPKM_bedfile_pan_number": "Pan4362",
 		"congenica_project": "5290",
 		"RPKM_also_analyse": vcp3_panel_list,
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
 	},
 	"Pan4396": { #ArcherDx
 		"archerdx": True,
@@ -1087,9 +1087,9 @@
 		"congenica_credentials": "STG",
 		"congenica_IR_template":"non-priority",
 		"congenica_project": "4201",
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
 	},
 	"Pan4827": {  # VCP3 STG R57
 		"mokapipe": True,
@@ -1099,9 +1099,9 @@
 		"congenica_credentials": "STG",
 		"congenica_IR_template":"non-priority",
 		"congenica_project": "4201",
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
 	},
 	"Pan4828": {  # VCP3 STG R58
 		"mokapipe": True,
@@ -1111,9 +1111,9 @@
 		"congenica_credentials": "STG",
 		"congenica_IR_template":"non-priority",
 		"congenica_project": "4201",
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
 	},
 	"Pan4829": {  # VCP3 STG R60
 		"mokapipe": True,
@@ -1123,9 +1123,9 @@
 		"congenica_credentials": "STG",
 		"congenica_IR_template":"non-priority",
 		"congenica_project": "4201",
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
 	},
 	"Pan4830": {  # VCP3 STG R62
 		"mokapipe": True,
@@ -1135,9 +1135,9 @@
 		"congenica_credentials": "STG",
 		"congenica_IR_template":"non-priority",
 		"congenica_project": "4201",
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
 	},
 	"Pan4831": {  # VCP3 STG R66
 		"mokapipe": True,
@@ -1147,9 +1147,9 @@
 		"congenica_credentials": "STG",
 		"congenica_IR_template":"non-priority",
 		"congenica_project": "4201",
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
 	},
 	"Pan4832": {  # VCP3 STG R78
 		"mokapipe": True,
@@ -1159,9 +1159,9 @@
 		"congenica_credentials": "STG",
 		"congenica_IR_template":"non-priority",
 		"congenica_project": "4201",
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
 	},
 	"Pan4833": {  # VCP3 STG R79
 		"mokapipe": True,
@@ -1171,9 +1171,9 @@
 		"congenica_credentials": "STG",
 		"congenica_IR_template":"non-priority",
 		"congenica_project": "4201",
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
 	},
 	"Pan4834": {  # VCP3 STG R81
 		"mokapipe": True,
@@ -1183,9 +1183,9 @@
 		"congenica_credentials": "STG",
 		"congenica_IR_template":"non-priority",
 		"congenica_project": "4201",
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
 	},
 	"Pan4835": {  # VCP3 STG R82
 		"mokapipe": True,
@@ -1195,9 +1195,9 @@
 		"congenica_credentials": "STG",
 		"congenica_IR_template":"non-priority",
 		"congenica_project": "4201",
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
 	},
 	"Pan4836": {  # VCP3 STG R229
 		"mokapipe": True,
@@ -1207,9 +1207,9 @@
 		"congenica_credentials": "STG",
 		"congenica_IR_template":"non-priority",
 		"congenica_project": "4201",
-		"hsmetrics_bedfile": "Pan4535data.bed",
-		"variant_calling_bedfile": "Pan4535data.bed",
-		"sambamba_bedfile": "Pan4535dataSambamba.bed",
+		"hsmetrics_bedfile": "Pan4995data.bed",
+		"variant_calling_bedfile": "Pan4995data.bed",
+		"sambamba_bedfile": "Pan4995dataSambamba.bed",
 	},
 	"Pan4818": {  # VCP2 STG R209
 		"mokapipe": True,