Refactor/pip freeze version

BALSAMIC/utils/constants.py

@@ -399,10 +399,11 @@
 
 umiworkflow_params = {
     "common": {
-        "align_header": "'@RG\\tID:Group\\tSM:{sample}\\tLB:TargetPanel\\tPL:ILLUMINA'",
+        "align_header":
+        "'@RG\\tID:Group\\tSM:{sample}\\tLB:TargetPanel\\tPL:ILLUMINA'",
         "align_intbases": 1000000,
         "filter_tumor_af": 0.0005
-	},
+    },
     "consensuscall": {
         "align_format": "BAM",
         "filter_minreads": "3,1,1",
@@ -422,6 +423,7 @@
         "vardict_filters": "-c 1 -S 2 -E 3 -g 4 -r 1 -F 0"
     },
     "vep": {
-	"vep_filters": "--compress_output bgzip --vcf --everything --allow_non_variant --dont_skip --buffer_size 10000 --format vcf --offline --variant_class --merged --cache --verbose --force_overwrite"
+        "vep_filters":
+        "--compress_output bgzip --vcf --everything --allow_non_variant --dont_skip --buffer_size 10000 --format vcf --offline --variant_class --merged --cache --verbose --force_overwrite"
     }
 }

BALSAMIC/utils/models.py

@@ -520,6 +520,7 @@ class UMIParamsConsensuscall(BaseModel):
     filter_minreads: str = '3,1,1'
     tag: str = 'XR'
 
+
 class UMIParamsTNscope(BaseModel):
     """This class defines the params settings used as constants in UMI workflow- rule tnscope.
 
@@ -538,6 +539,7 @@ class UMIParamsTNscope(BaseModel):
     prunefactor: int
     disable_detect: str
 
+
 class UMIParamsVardict(BaseModel):
     """This class defines the params settings used as constants in UMIworkflow-rule vardict.
 
@@ -546,6 +548,7 @@ class UMIParamsVardict(BaseModel):
     """
     vardict_filters: str
 
+
 class UMIParamsVEP(BaseModel):
     """This class defines the params settings used as constants in UMIworkflow-rule vep.
 
@@ -554,6 +557,7 @@ class UMIParamsVEP(BaseModel):
     """
     vep_filters: str
 
+
 class UMIworkflowConfig(BaseModel):
     """ Defines set of rules in UMI workflow.
 

requirements.txt

@@ -1,19 +1,19 @@
-click
-pyyaml
-yapf
-graphviz
-pygments
-coloredlogs
-psutil
-snakemake==5.13.0
-gsutil
-six>=1.12.0
-jinja2
-networkx
-colorclass
-pydantic
-numpy
+click>=7.1.2
+colorclass>=2.2.0
+coloredlogs>=14.0
 cyvcf2<0.10.0
+graphviz>=0.14
+gsutil>=4.50
+jinja2>=2.11.2
+matplotlib>=3.3.0
+networkx>=2.4
+numpy>=1.18.4
 pandas>1.1.0
+psutil>=5.7.0
+pydantic>=1.5.1
+pygments>=2.6.1
+pyyaml>=5.3.1
 seaborn>=0.11.0
-matplotlib>=3.3.0
+six>=1.12.0
+snakemake==5.13.0
+yapf>=0.30.0

tests/utils/test_models.py

@@ -286,13 +286,13 @@ def test_sample_instance_model():
 
 def test_umiparams_common():
     """ test UMIParamsCommon model for correct validation """
-        
+
     # GIVEN a UMI workflow common params
     test_commonparams = {
         "align_header": "test_header_name",
         "align_intbases": 100,
         "filter_tumor_af": 0.01
-    }    
+    }
     # WHEN building the model
     test_commonparams_built = UMIParamsCommon(**test_commonparams)
     # THEN assert values
@@ -304,9 +304,7 @@ def test_umiparams_common():
 def test_umiparams_umiextract():
     """ test UMIParamsUMIextract model for correct validation """
     # GIVEN umiextract params
-    test_umiextractparams = {
-        "read_structure": "['mode', 'r1,r2']"
-    }
+    test_umiextractparams = {"read_structure": "['mode', 'r1,r2']"}
 
     # WHEN building the model
     test_umiextractparams_built = UMIParamsUMIextract(**test_umiextractparams)
@@ -320,17 +318,17 @@ def test_umiparams_consensuscall():
 
     #GIVEN consensuscall params
     test_consensuscall = {
-        "align_format":"BAM",
-    	"filter_minreads":"6,3,3",
-    	"tag":"XZ"
+        "align_format": "BAM",
+        "filter_minreads": "6,3,3",
+        "tag": "XZ"
     }
-    
+
     #WHEN building the model
     test_consensuscall_built = UMIParamsConsensuscall(**test_consensuscall)
-	
+
     #THEN assert values
     assert test_consensuscall_built.align_format == "BAM"
-    assert test_consensuscall_built.filter_minreads == "6,3,3" 
+    assert test_consensuscall_built.filter_minreads == "6,3,3"
     assert test_consensuscall_built.tag == "XZ"
 
 
@@ -343,9 +341,9 @@ def test_umiparams_tnscope():
         "min_tumorLOD": 6,
         "error_rate": 5,
         "prunefactor": 3,
-        "disable_detect":"abc"
+        "disable_detect": "abc"
     }
-    
+
     #WHEN building the model
     test_tnscope_params_built = UMIParamsTNscope(**test_tnscope_params)
 
@@ -356,13 +354,12 @@ def test_umiparams_tnscope():
     assert test_tnscope_params_built.prunefactor == 3
     assert test_tnscope_params_built.disable_detect == "abc"
 
+
 def test_umiparams_vardict():
     """ test UMIParamsVardict model for correct validation"""
 
     #GIVEN vardict params
-    test_umivardict={ 
-        "vardict_filters": "-a 1 -b 2 -c 5"
-    }
+    test_umivardict = {"vardict_filters": "-a 1 -b 2 -c 5"}
 
     #WHEN building the model
     test_umivardict_built = UMIParamsVardict(**test_umivardict)
@@ -375,9 +372,7 @@ def test_umiparams_vep():
     """ test UMIParamsVEP model for correct validation"""
 
     #GIVEN vardict params
-    test_umivep={
-        "vep_filters": "all defaults params"
-    }
+    test_umivep = {"vep_filters": "all defaults params"}
 
     #WHEN building the model
     test_umivep_built = UMIParamsVEP(**test_umivep)