Merge pull request #99 from jiaan-yu/fix-bug

Fix bug

Author: junyk

janis_bioinformatics/tools/common/filtervardictsomaticvcf.py

@@ -37,7 +37,7 @@ def base_command(self):
 
     def inputs(self) -> List[ToolInput]:
         return [
-            ToolInput("vcf", Vcf(optional=True), position=1),
+            ToolInput("vcf", Vcf(), position=1),
             ToolInput(
                 "outputFilename",
                 Filename(
@@ -47,12 +47,17 @@ def inputs(self) -> List[ToolInput]:
                 ),
                 prefix="-o",
                 position=3,
-                shell_quote=False,
             ),
         ]
 
     def outputs(self) -> List[ToolOutput]:
-        return [ToolOutput("out", Vcf, glob=InputSelector("outputFilename"),)]
+        return [
+            ToolOutput(
+                "out",
+                Vcf(),
+                InputSelector("outputFilename"),
+            )
+        ]
 
     def arguments(self):
         return [

janis_bioinformatics/tools/variantcallers/vardictgermline_variants.py

@@ -46,7 +46,6 @@ def constructor(self):
                 var2vcfSampleName=self.sample_name,
                 alleleFreqThreshold=self.allele_freq_threshold,
                 var2vcfAlleleFreqThreshold=self.allele_freq_threshold,
-                chromNamesAreNumbers=True,
                 vcfFormat=True,
                 chromColumn=1,
                 regStartCol=2,

janis_bioinformatics/tools/variantcallers/vardictsomatic_variants.py

@@ -49,7 +49,6 @@ def constructor(self):
                 normalName=self.normal_name,
                 tumorName=self.tumor_name,
                 alleleFreqThreshold=self.allele_freq_threshold,
-                chromNamesAreNumbers=True,
                 vcfFormat=True,
                 chromColumn=1,
                 regStartCol=2,