Merge branch 'master' of github.com:PMCC-BioinformaticsCore/janis-bioinformatics

Author: illusional

janis_bioinformatics/tools/dawson/workflows/mutectjointsomaticworkflow.py

@@ -9,18 +9,22 @@
     BcfToolsNorm_1_9 as BcfToolsNorm,
 )
 from janis_bioinformatics.tools.dawson.createcallregions.base import CreateCallRegions
+
+# these dont need cram, because they dont work on crams
 from janis_bioinformatics.tools.gatk4 import (
     Gatk4CalculateContaminationLatest as CalculateContamination,
     Gatk4FilterMutectCallsLatest as FilterMutectCalls,
     Gatk4LearnReadOrientationModelLatest as LearnReadOrientationModel,
     Gatk4MergeMutectStatsLatest as MergeMutectStats,
 )
+
+# for these we need the special cram version because they work directly on the cram
 from janis_bioinformatics.tools.gatk4.mutect2.versions import (
-    GatkMutect2Cram_4_1_6 as Mutect2,
+    GatkMutect2Cram_4_1_8 as Mutect2,
 )
 
 from janis_bioinformatics.tools.gatk4.getpileupsummaries.versions import (
-    Gatk4GetPileUpSummariesCram_4_1_6 as GetPileUpSummaries,
+    Gatk4GetPileUpSummariesCram_4_1_8 as GetPileUpSummaries,
 )
 
 

janis_bioinformatics/tools/gatk4/calculatecontaminations/versions.py

@@ -1,5 +1,12 @@
 from .base import Gatk4CalculateContaminationBase
-from ..versions import Gatk_4_1_2_0, Gatk_4_1_3_0, Gatk_4_1_4_0
+from ..versions import (
+    Gatk_4_1_2_0,
+    Gatk_4_1_3_0,
+    Gatk_4_1_4_0,
+    Gatk_4_1_6_0,
+    Gatk_4_1_7_0,
+    Gatk_4_1_8_1,
+)
 
 
 class Gatk4CalculateContamination_4_1_2(Gatk_4_1_2_0, Gatk4CalculateContaminationBase):
@@ -14,7 +21,19 @@ class Gatk4CalculateContamination_4_1_4(Gatk_4_1_4_0, Gatk4CalculateContaminatio
     pass
 
 
-Gatk4CalculateContaminationLatest = Gatk4CalculateContamination_4_1_4
+class Gatk4CalculateContamination_4_1_6(Gatk_4_1_6_0, Gatk4CalculateContaminationBase):
+    pass
+
+
+class Gatk4CalculateContamination_4_1_7(Gatk_4_1_7_0, Gatk4CalculateContaminationBase):
+    pass
+
+
+class Gatk4CalculateContamination_4_1_8(Gatk_4_1_8_1, Gatk4CalculateContaminationBase):
+    pass
+
+
+Gatk4CalculateContaminationLatest = Gatk4CalculateContamination_4_1_8
 
 if __name__ == "__main__":
     print(Gatk4CalculateContaminationBase().help())

janis_bioinformatics/tools/gatk4/filtermutectcalls/versions.py

@@ -1,5 +1,12 @@
 from .base import Gatk4FilterMutectCallsBase
-from ..versions import Gatk_4_1_2_0, Gatk_4_1_3_0, Gatk_4_1_4_0
+from ..versions import (
+    Gatk_4_1_2_0,
+    Gatk_4_1_3_0,
+    Gatk_4_1_4_0,
+    Gatk_4_1_6_0,
+    Gatk_4_1_7_0,
+    Gatk_4_1_8_1,
+)
 
 
 class Gatk4FilterMutectCalls_4_1_2(Gatk_4_1_2_0, Gatk4FilterMutectCallsBase):
@@ -14,7 +21,19 @@ class Gatk4FilterMutectCalls_4_1_4(Gatk_4_1_4_0, Gatk4FilterMutectCallsBase):
     pass
 
 
-Gatk4FilterMutectCallsLatest = Gatk4FilterMutectCalls_4_1_3
+class Gatk4FilterMutectCalls_4_1_6(Gatk_4_1_6_0, Gatk4FilterMutectCallsBase):
+    pass
+
+
+class Gatk4FilterMutectCalls_4_1_7(Gatk_4_1_7_0, Gatk4FilterMutectCallsBase):
+    pass
+
+
+class Gatk4FilterMutectCalls_4_1_8(Gatk_4_1_8_1, Gatk4FilterMutectCallsBase):
+    pass
+
+
+Gatk4FilterMutectCallsLatest = Gatk4FilterMutectCalls_4_1_8
 
 if __name__ == "__main__":
     print(Gatk4FilterMutectCallsBase().help())

janis_bioinformatics/tools/gatk4/getpileupsummaries/versions.py

@@ -1,6 +1,13 @@
 from .base import Gatk4GetPileUpSummariesBase
 from .base_cram import Gatk4GetPileUpSummariesCramBase
-from ..versions import Gatk_4_1_2_0, Gatk_4_1_3_0, Gatk_4_1_4_0, Gatk_4_1_6_0
+from ..versions import (
+    Gatk_4_1_2_0,
+    Gatk_4_1_3_0,
+    Gatk_4_1_4_0,
+    Gatk_4_1_6_0,
+    Gatk_4_1_7_0,
+    Gatk_4_1_8_1,
+)
 
 
 class Gatk4GetPileUpSummaries_4_1_2(Gatk_4_1_2_0, Gatk4GetPileUpSummariesBase):
@@ -19,6 +26,15 @@ class Gatk4GetPileUpSummaries_4_1_6(Gatk_4_1_6_0, Gatk4GetPileUpSummariesBase):
     pass
 
 
+class Gatk4GetPileUpSummaries_4_1_7(Gatk_4_1_7_0, Gatk4GetPileUpSummariesBase):
+    pass
+
+
+class Gatk4GetPileUpSummaries_4_1_8(Gatk_4_1_8_1, Gatk4GetPileUpSummariesBase):
+    pass
+
+
+# cram versions
 class Gatk4GetPileUpSummariesCram_4_1_2(Gatk_4_1_2_0, Gatk4GetPileUpSummariesCramBase):
     pass
 
@@ -35,7 +51,15 @@ class Gatk4GetPileUpSummariesCram_4_1_6(Gatk_4_1_6_0, Gatk4GetPileUpSummariesCra
     pass
 
 
-Gatk4GetPileUpSummariesLatest = Gatk4GetPileUpSummaries_4_1_6
+class Gatk4GetPileUpSummariesCram_4_1_7(Gatk_4_1_7_0, Gatk4GetPileUpSummariesCramBase):
+    pass
+
+
+class Gatk4GetPileUpSummariesCram_4_1_8(Gatk_4_1_8_1, Gatk4GetPileUpSummariesCramBase):
+    pass
+
+
+Gatk4GetPileUpSummariesLatest = Gatk4GetPileUpSummaries_4_1_8
 
 if __name__ == "__main__":
     print(Gatk4GetPileUpSummariesBase().help())

janis_bioinformatics/tools/gatk4/learnreadorientationmodel/versions.py

@@ -1,5 +1,12 @@
-from ..versions import Gatk_4_1_2_0, Gatk_4_1_3_0, Gatk_4_1_4_0
 from .base import Gatk4LearnReadOrientationModelBase
+from ..versions import (
+    Gatk_4_1_2_0,
+    Gatk_4_1_3_0,
+    Gatk_4_1_4_0,
+    Gatk_4_1_6_0,
+    Gatk_4_1_7_0,
+    Gatk_4_1_8_1,
+)
 
 
 class Gatk4LearnReadOrientationModel_4_1_2(
@@ -20,7 +27,25 @@ class Gatk4LearnReadOrientationModel_4_1_4(
     pass
 
 
-Gatk4LearnReadOrientationModelLatest = Gatk4LearnReadOrientationModel_4_1_4
+class Gatk4LearnReadOrientationModel_4_1_6(
+    Gatk_4_1_6_0, Gatk4LearnReadOrientationModelBase
+):
+    pass
+
+
+class Gatk4LearnReadOrientationModel_4_1_7(
+    Gatk_4_1_7_0, Gatk4LearnReadOrientationModelBase
+):
+    pass
+
+
+class Gatk4LearnReadOrientationModel_4_1_8(
+    Gatk_4_1_8_1, Gatk4LearnReadOrientationModelBase
+):
+    pass
+
+
+Gatk4LearnReadOrientationModelLatest = Gatk4LearnReadOrientationModel_4_1_8
 
 if __name__ == "__main__":
     print(Gatk4LearnReadOrientationModelBase().help())

janis_bioinformatics/tools/gatk4/mergemutectstats/versions.py

@@ -1,5 +1,12 @@
 from .base import Gatk4MergeMutectStatsBase
-from ..versions import Gatk_4_1_2_0, Gatk_4_1_3_0, Gatk_4_1_4_0
+from ..versions import (
+    Gatk_4_1_2_0,
+    Gatk_4_1_3_0,
+    Gatk_4_1_4_0,
+    Gatk_4_1_6_0,
+    Gatk_4_1_7_0,
+    Gatk_4_1_8_1,
+)
 
 
 class Gatk4MergeMutectStats_4_1_2(Gatk_4_1_2_0, Gatk4MergeMutectStatsBase):
@@ -14,7 +21,19 @@ class Gatk4MergeMutectStats_4_1_4(Gatk_4_1_4_0, Gatk4MergeMutectStatsBase):
     pass
 
 
-Gatk4MergeMutectStatsLatest = Gatk4MergeMutectStats_4_1_4
+class Gatk4MergeMutectStats_4_1_6(Gatk_4_1_6_0, Gatk4MergeMutectStatsBase):
+    pass
+
+
+class Gatk4MergeMutectStats_4_1_7(Gatk_4_1_7_0, Gatk4MergeMutectStatsBase):
+    pass
+
+
+class Gatk4MergeMutectStats_4_1_8(Gatk_4_1_8_1, Gatk4MergeMutectStatsBase):
+    pass
+
+
+Gatk4MergeMutectStatsLatest = Gatk4MergeMutectStats_4_1_8
 
 if __name__ == "__main__":
     print(Gatk4MergeMutectStatsBase().help())