backmap_workflow issueshttps://git.computational.bio.uni-giessen.de/tbg/backmap_workflow/-/issues2021-01-07T14:00:15Zhttps://git.computational.bio.uni-giessen.de/tbg/backmap_workflow/-/issues/1Linting2021-01-07T14:00:15ZRaphael Müllerraphael.mueller@computational.bio.uni-giessen.deLinting- [x] 0 info The tab character is not allowed in source files NoTabCharacter
- [x] 2 info File backmap.nf has consecutive blank lines ConsecutiveBlankLines
- [x] 4 info Class should be marked with one of @Gra...- [x] 0 info The tab character is not allowed in source files NoTabCharacter
- [x] 2 info File backmap.nf has consecutive blank lines ConsecutiveBlankLines
- [x] 4 info Class should be marked with one of @GrailsCompileStatic, @CompileStatic or @CompileDynamic CompileStatic
- [x] 4 info The String 'v0.4' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 12 info Line ends with whitespace characters TrailingWhitespace
- [x] 15 info Line ends with whitespace characters TrailingWhitespace
- [x] 20 info Line ends with whitespace characters TrailingWhitespace
- [x] 27 info Line ends with whitespace characters TrailingWhitespace
- [x] 31 info File backmap.nf has consecutive blank lines ConsecutiveBlankLines
- [x] 41 info Line ends with whitespace characters TrailingWhitespace
- [x] 60 info File backmap.nf has consecutive blank lines ConsecutiveBlankLines
- [x] 63 info Line ends with whitespace characters TrailingWhitespace
- [x] 73 info The String 'assembly' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 75 info Duplicate String Literal: NO_FILE DuplicateStringLiteral
- [x] 75 info The String 'single-end' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 76 info Duplicate String Literal: NO_FILE DuplicateStringLiteral
- [x] 76 info The String 'paired-end' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 77 info Duplicate String Literal: NO_FILE DuplicateStringLiteral
- [x] 77 info The String 'pacbio' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 78 info Duplicate String Literal: NO_FILE DuplicateStringLiteral
- [x] 78 info The String 'nanopore' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 80 info Duplicate String Literal: NO_FILE DuplicateStringLiteral
- [x] 80 info The String 'illumina-bam-files' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 81 info Duplicate String Literal: NO_FILE DuplicateStringLiteral
- [x] 81 info The String 'pacbio-bam-files' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 82 info Duplicate String Literal: NO_FILE DuplicateStringLiteral
- [x] 82 info The String 'nanopore-bam-files' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 84 info The String 'file-separator' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 84 info The String ',' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 86 info The String 'output' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 87 info The String 'prefix' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 87 info The String 'tbg_backmap' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 88 info The String 'threads' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 90 info The String 'keep-temporary' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 91 info The String 'help' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 92 info The String 'version' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 93 info The String 'debug' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 95 info The String 'skip-quality-control' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 96 info The String 'skip-coverage-histogram' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 97 info The String 'skip-genome-size-estimation' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 99 info The String 'bwa-options' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 99 info The String '-a -c 10000' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 100 info The String 'minimap-pacbio-options' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 100 info The String '-H' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 101 info The String 'minimap-nanopore-options' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 101 info The String '' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 102 info The String 'qualimap-options' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 102 info The String '' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 104 info Duplicate String Literal: assembly DuplicateStringLiteral
- [x] 104 info The String 'assembly' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 105 info Duplicate String Literal: single-end DuplicateStringLiteral
- [x] 105 info The String 'single-end' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 106 info Duplicate String Literal: paired-end DuplicateStringLiteral
- [x] 106 info Line ends with whitespace characters TrailingWhitespace
- [x] 106 info The String 'paired-end' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 107 info Duplicate String Literal: pacbio DuplicateStringLiteral
- [x] 107 info Line ends with whitespace characters TrailingWhitespace
- [x] 107 info The String 'pacbio' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 108 info Duplicate String Literal: nanopore DuplicateStringLiteral
- [x] 108 info Line ends with whitespace characters TrailingWhitespace
- [x] 108 info The String 'nanopore' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 110 info Duplicate String Literal: illumina-bam-files DuplicateStringLiteral
- [x] 110 info Line ends with whitespace characters TrailingWhitespace
- [x] 110 info The String 'illumina-bam-files' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 111 info Duplicate String Literal: pacbio-bam-files DuplicateStringLiteral
- [x] 111 info Line ends with whitespace characters TrailingWhitespace
- [x] 111 info The String 'pacbio-bam-files' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 112 info Duplicate String Literal: nanopore-bam-files DuplicateStringLiteral
- [x] 112 info Line ends with whitespace characters TrailingWhitespace
- [x] 112 info The String 'nanopore-bam-files' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 114 info Duplicate String Literal: file-separator DuplicateStringLiteral
- [x] 114 info The String 'file-separator' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 116 info Duplicate String Literal: output DuplicateStringLiteral
- [x] 116 info The String 'output' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 117 info Duplicate String Literal: prefix DuplicateStringLiteral
- [x] 117 info The String 'prefix' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 118 info Duplicate String Literal: threads DuplicateStringLiteral
- [x] 118 info The String 'threads' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 120 info Duplicate String Literal: bwa-options DuplicateStringLiteral
- [x] 120 info The String 'bwa-options' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 121 info Duplicate String Literal: minimap-pacbio-options DuplicateStringLiteral
- [x] 121 info The String 'minimap-pacbio-options' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 122 info Duplicate String Literal: minimap-nanopore-options DuplicateStringLiteral
- [x] 122 info The String 'minimap-nanopore-options' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 123 info Duplicate String Literal: qualimap-options DuplicateStringLiteral
- [x] 123 info The String 'qualimap-options' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 125 info Duplicate String Literal: keep-temporary DuplicateStringLiteral
- [x] 125 info The String 'keep-temporary' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 126 info Duplicate String Literal: help DuplicateStringLiteral
- [x] 126 info The String 'help' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 127 info Duplicate String Literal: version DuplicateStringLiteral
- [x] 127 info The String 'version' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 128 info Duplicate String Literal: debug DuplicateStringLiteral
- [x] 128 info The String 'debug' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 130 info Duplicate String Literal: skip-quality-control DuplicateStringLiteral
- [x] 130 info The String 'skip-quality-control' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 131 info Duplicate String Literal: skip-coverage-histogram DuplicateStringLiteral
- [x] 131 info The String 'skip-coverage-histogram' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 132 info Duplicate String Literal: skip-genome-size-estimation DuplicateStringLiteral
- [x] 132 info The String 'skip-genome-size-estimation' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 134 info Duplicate String Literal: NO_FILE DuplicateStringLiteral
- [x] 135 info Duplicate String Literal: NO_FILE DuplicateStringLiteral
- [x] 136 info Duplicate String Literal: NO_FILE DuplicateStringLiteral
- [x] 137 info Duplicate String Literal: NO_FILE DuplicateStringLiteral
- [x] 138 info Duplicate String Literal: NO_FILE DuplicateStringLiteral
- [x] 139 info Duplicate String Literal: NO_FILE DuplicateStringLiteral
- [x] 139 info Line ends with whitespace characters TrailingWhitespace
- [x] 140 info Duplicate String Literal: NO_FILE DuplicateStringLiteral
- [x] 140 info Line ends with whitespace characters TrailingWhitespace
- [x] 141 info Duplicate String Literal: NO_FILE DuplicateStringLiteral
- [x] 141 info Line ends with whitespace characters TrailingWhitespace
- [x] 145 warning The expression (!!keepTemporaryFiles) is a confusing double negative DoubleNegative
- [x] 145 warning The expression (!!keepTemporaryFiles) in class None contains confusing multiple consecutive unary operators MultipleUnaryOperators
- [x] 146 warning The expression (!!printHelp) is a confusing double negative DoubleNegative
- [x] 146 warning The expression (!!printHelp) in class None contains confusing multiple consecutive unary operators MultipleUnaryOperators
- [x] 147 warning The expression (!!printVersion) is a confusing double negative DoubleNegative
- [x] 147 warning The expression (!!printVersion) in class None contains confusing multiple consecutive unary operators MultipleUnaryOperators
- [x] 149 info Line ends with whitespace characters TrailingWhitespace
- [x] 150 info Line ends with whitespace characters TrailingWhitespace
- [x] 151 info Line ends with whitespace characters TrailingWhitespace
- [x] 153 info The if keyword within class None is not followed by a single space SpaceAfterIf
- [x] 153 info The opening brace for the block in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 154 info The statement on line 154 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 154 info The String 'Files:' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 155 info The statement on line 155 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 155 info Line ends with whitespace characters TrailingWhitespace
- [x] 156 info The statement on line 156 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 156 info Line ends with whitespace characters TrailingWhitespace
- [x] 157 info The statement on line 157 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 157 info Line ends with whitespace characters TrailingWhitespace
- [x] 158 info The statement on line 158 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 158 info Line ends with whitespace characters TrailingWhitespace
- [x] 159 info The statement on line 159 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 159 info Line ends with whitespace characters TrailingWhitespace
- [x] 160 info The statement on line 160 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 161 info The statement on line 161 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 162 info The statement on line 162 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 163 info The statement on line 163 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 163 info The String '' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 164 info The statement on line 164 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 164 info The String 'Additional Tool Options:' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 165 info The statement on line 165 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 166 info The statement on line 166 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 167 info The statement on line 167 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 168 info The statement on line 168 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 169 info The statement on line 169 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 169 info The String '' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 170 info The statement on line 170 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 170 info The String 'Control flow instructions:' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 171 info The statement on line 171 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 172 info The statement on line 172 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 173 info The statement on line 173 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 174 info The statement on line 174 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 174 info The String 'Misc:' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 175 info The statement on line 175 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 176 info The statement on line 176 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 177 info The statement on line 177 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 178 info The statement on line 178 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 179 info The statement on line 179 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 180 info The statement on line 180 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 181 info The statement on line 181 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 182 info The statement on line 182 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 183 info The statement on line 183 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 183 info The String '' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 184 info The statement on line 184 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 184 info The String 'Inner Boolean Vars:' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 185 info The statement on line 185 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 186 info The statement on line 186 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 187 info The statement on line 187 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 188 info The statement on line 188 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 189 info The statement on line 189 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 190 info The statement on line 190 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 191 info The statement on line 191 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 192 info The statement on line 192 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 193 info The statement on line 193 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 194 info The statement on line 194 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 194 info The String '' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 197 info The if keyword within class None is not followed by a single space SpaceAfterIf
- [x] 197 info The opening brace for the block in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 198 info The statement on line 198 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 199 info The statement on line 199 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 202 info The if keyword within class None is not followed by a single space SpaceAfterIf
- [x] 202 info The opening brace for the block in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 203 info The statement on line 203 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 204 info The statement on line 204 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 208 warning Variable named BWAINDEX in class None does not match the pattern [a-z][a-zA-Z0-9]* VariableName
- [x] 214 info The closing brace for the block in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 214 info The if keyword within class None is not followed by a single space SpaceAfterIf
- [x] 214 info The opening brace for the block in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 215 info Code block starts with a blank line. BlockStartsWithBlankLine
- [x] 216 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 216 info The statement on line 216 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 216 warning The line exceeds 120 characters. The line is 162 characters. LineLength
- [x] 216 info The opening brace for the closure in class None is not followed by a space or whitespace SpaceAfterOpeningBrace
- [x] 216 info The opening brace for the closure in class None is not followed by a space or whitespace SpaceAfterOpeningBrace
- [x] 216 info The closing brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeClosingBrace
- [x] 216 info The closing brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeClosingBrace
- [x] 216 info The opening brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 216 info The opening brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 217 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 217 info The statement on line 217 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 217 warning The line exceeds 120 characters. The line is 162 characters. LineLength
- [x] 217 info The opening brace for the closure in class None is not followed by a space or whitespace SpaceAfterOpeningBrace
- [x] 217 info The opening brace for the closure in class None is not followed by a space or whitespace SpaceAfterOpeningBrace
- [x] 217 info The closing brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeClosingBrace
- [x] 217 info The closing brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeClosingBrace
- [x] 217 info The opening brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 217 info The opening brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 218 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 218 info The statement on line 218 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 218 warning The line exceeds 120 characters. The line is 162 characters. LineLength
- [x] 218 info The opening brace for the closure in class None is not followed by a space or whitespace SpaceAfterOpeningBrace
- [x] 218 info The opening brace for the closure in class None is not followed by a space or whitespace SpaceAfterOpeningBrace
- [x] 218 info The closing brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeClosingBrace
- [x] 218 info The closing brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeClosingBrace
- [x] 218 info The opening brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 218 info The opening brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 219 info Code block ends with a blank line. BlockEndsWithBlankLine
- [x] 220 info The if keyword within class None is not followed by a single space SpaceAfterIf
- [x] 220 info The opening brace for the block in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 222 info The statement on line 222 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 223 info The statement on line 223 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 225 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 225 info The statement on line 225 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 225 warning The line exceeds 120 characters. The line is 164 characters. LineLength
- [x] 225 info The opening brace for the closure in class None is not followed by a space or whitespace SpaceAfterOpeningBrace
- [x] 225 info The opening brace for the closure in class None is not followed by a space or whitespace SpaceAfterOpeningBrace
- [x] 225 info The closing brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeClosingBrace
- [x] 225 info The closing brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeClosingBrace
- [x] 225 info The opening brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 225 info The opening brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 226 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 226 info The statement on line 226 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 226 warning The line exceeds 120 characters. The line is 164 characters. LineLength
- [x] 226 info The opening brace for the closure in class None is not followed by a space or whitespace SpaceAfterOpeningBrace
- [x] 226 info The opening brace for the closure in class None is not followed by a space or whitespace SpaceAfterOpeningBrace
- [x] 226 info The closing brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeClosingBrace
- [x] 226 info The closing brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeClosingBrace
- [x] 226 info The opening brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 226 info The opening brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 227 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 227 info The statement on line 227 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 227 warning The line exceeds 120 characters. The line is 164 characters. LineLength
- [x] 227 info The opening brace for the closure in class None is not followed by a space or whitespace SpaceAfterOpeningBrace
- [x] 227 info The opening brace for the closure in class None is not followed by a space or whitespace SpaceAfterOpeningBrace
- [x] 227 info The closing brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeClosingBrace
- [x] 227 info The closing brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeClosingBrace
- [x] 227 info The opening brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 227 info The opening brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 228 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 228 info The statement on line 228 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 228 warning The line exceeds 120 characters. The line is 164 characters. LineLength
- [x] 228 info The opening brace for the closure in class None is not followed by a space or whitespace SpaceAfterOpeningBrace
- [x] 228 info The opening brace for the closure in class None is not followed by a space or whitespace SpaceAfterOpeningBrace
- [x] 228 info The closing brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeClosingBrace
- [x] 228 info The closing brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeClosingBrace
- [x] 228 info The opening brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 228 info The opening brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 231 info The statement on line 231 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 231 info The closing brace for the closure in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 232 info The statement on line 232 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 232 info The String '*{amb,ann,bwt,pac,sa}' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 233 info Duplicate String Literal: copy DuplicateStringLiteral
- [x] 233 info The statement on line 233 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 233 info The String '*.{log,err}' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 234 info The statement on line 234 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 236 info The statement on line 236 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 238 info The statement on line 238 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 239 info The statement on line 239 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 241 info The statement on line 241 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 246 info Line ends with whitespace characters TrailingWhitespace
- [x] 247 info The statement on line 247 in class None is at the incorrect indent level: Expected column 5 but was 4 Indentation
- [x] 247 info The closing brace for the closure in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 248 info The statement on line 248 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 249 info The statement on line 249 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 249 info The if keyword within class None is not followed by a single space SpaceAfterIf
- [x] 249 info The opening brace for the block in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 250 info Duplicate String Literal: copy DuplicateStringLiteral
- [x] 250 info The statement on line 250 in class None is at the incorrect indent level: Expected column 13 but was 7 Indentation
- [x] 253 info The statement on line 253 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 254 info The statement on line 254 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 256 info The statement on line 256 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 257 info The statement on line 257 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 257 info The String '*.err' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 259 info The statement on line 259 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 260 warning The line exceeds 120 characters. The line is 161 characters. LineLength
- [x] 265 info The statement on line 265 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 265 info The closing brace for the closure in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 266 info Duplicate Number Literal: 8 DuplicateNumberLiteral
- [x] 266 info The statement on line 266 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 267 info The statement on line 267 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 267 info The if keyword within class None is not followed by a single space SpaceAfterIf
- [x] 267 info The opening brace for the block in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 268 warning Map [mode:copy] is duplicated. DuplicateMapLiteral
- [x] 268 info Duplicate String Literal: copy DuplicateStringLiteral
- [x] 268 info The statement on line 268 in class None is at the incorrect indent level: Expected column 13 but was 7 Indentation
- [x] 271 info The statement on line 271 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 272 info The statement on line 272 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 274 info The statement on line 274 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 275 info Duplicate String Literal: *.err DuplicateStringLiteral
- [x] 275 info The statement on line 275 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 275 info The String '*.err' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 278 warning The line exceeds 120 characters. The line is 159 characters. LineLength
- [x] 282 info The statement on line 282 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 285 info The statement on line 285 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 285 info The closing brace for the closure in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 286 info The statement on line 286 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 286 info The if keyword within class None is not followed by a single space SpaceAfterIf
- [x] 286 info The opening brace for the block in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 287 warning Map [mode:copy] is duplicated. DuplicateMapLiteral
- [x] 287 info Duplicate String Literal: copy DuplicateStringLiteral
- [x] 287 info The statement on line 287 in class None is at the incorrect indent level: Expected column 13 but was 7 Indentation
- [x] 289 info Duplicate Number Literal: 8 DuplicateNumberLiteral
- [x] 289 info The statement on line 289 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 291 info The statement on line 291 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 292 info The statement on line 292 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 294 info The statement on line 294 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 295 info Duplicate String Literal: *.err DuplicateStringLiteral
- [x] 295 info The statement on line 295 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 295 info The String '*.err' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 297 info The statement on line 297 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 298 warning The line exceeds 120 characters. The line is 171 characters. LineLength
- [x] 303 info The statement on line 303 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 303 info The closing brace for the closure in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 304 info The statement on line 304 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 304 info The if keyword within class None is not followed by a single space SpaceAfterIf
- [x] 304 info The opening brace for the block in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 305 warning Map [mode:copy] is duplicated. DuplicateMapLiteral
- [x] 305 info Duplicate String Literal: copy DuplicateStringLiteral
- [x] 305 info The statement on line 305 in class None is at the incorrect indent level: Expected column 13 but was 7 Indentation
- [x] 307 info Duplicate Number Literal: 8 DuplicateNumberLiteral
- [x] 307 info The statement on line 307 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 309 info The statement on line 309 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 310 info The statement on line 310 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 312 info The statement on line 312 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 313 info Duplicate String Literal: *.err DuplicateStringLiteral
- [x] 313 info The statement on line 313 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 313 info The String '*.err' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 315 info The statement on line 315 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 316 warning The line exceeds 120 characters. The line is 175 characters. LineLength
- [x] 320 info The statement on line 320 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 320 info The String 'specify either reads to map with assembly or already mapped reads' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 321 info The statement on line 321 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 322 info The statement on line 322 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 326 info The closing brace for the closure in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 327 info The statement on line 327 in class None is at the incorrect indent level: Expected one of columns [5, 9, 13] but was 3 Indentation
- [x] 327 info The if keyword within class None is not followed by a single space SpaceAfterIf
- [x] 327 info The opening brace for the block in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 328 warning Map [mode:copy] is duplicated. DuplicateMapLiteral
- [x] 328 info Duplicate String Literal: copy DuplicateStringLiteral
- [x] 328 info The statement on line 328 in class None is at the incorrect indent level: Expected column 9 but was 5 Indentation
- [x] 330 info Duplicate Number Literal: 8 DuplicateNumberLiteral
- [x] 330 info The statement on line 330 in class None is at the incorrect indent level: Expected one of columns [5, 9, 13] but was 3 Indentation
- [x] 334 info The String 'Illumina' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 342 info The closing brace for the closure in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 343 info The statement on line 343 in class None is at the incorrect indent level: Expected one of columns [5, 9, 13] but was 3 Indentation
- [x] 343 info The if keyword within class None is not followed by a single space SpaceAfterIf
- [x] 343 info The opening brace for the block in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 344 warning Map [mode:copy] is duplicated. DuplicateMapLiteral
- [x] 344 info Duplicate String Literal: copy DuplicateStringLiteral
- [x] 344 info The statement on line 344 in class None is at the incorrect indent level: Expected column 9 but was 5 Indentation
- [x] 346 info Duplicate Number Literal: 8 DuplicateNumberLiteral
- [x] 346 info The statement on line 346 in class None is at the incorrect indent level: Expected one of columns [5, 9, 13] but was 3 Indentation
- [x] 350 info The String 'Pacbio' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 358 info The closing brace for the closure in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 359 info The statement on line 359 in class None is at the incorrect indent level: Expected one of columns [5, 9, 13] but was 3 Indentation
- [x] 359 info The if keyword within class None is not followed by a single space SpaceAfterIf
- [x] 359 info The opening brace for the block in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 360 warning Map [mode:copy] is duplicated. DuplicateMapLiteral
- [x] 360 info Duplicate String Literal: copy DuplicateStringLiteral
- [x] 360 info The statement on line 360 in class None is at the incorrect indent level: Expected column 9 but was 5 Indentation
- [x] 362 info Duplicate Number Literal: 8 DuplicateNumberLiteral
- [x] 362 info The statement on line 362 in class None is at the incorrect indent level: Expected one of columns [5, 9, 13] but was 3 Indentation
- [x] 366 info The String 'Nanopore' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 374 info The closing brace for the closure in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 375 warning Map [mode:copy] is duplicated. DuplicateMapLiteral
- [x] 375 info Duplicate String Literal: copy DuplicateStringLiteral
- [x] 375 info The statement on line 375 in class None is at the incorrect indent level: Expected one of columns [5, 9, 13] but was 3 Indentation
- [x] 377 info Duplicate Number Literal: 8 DuplicateNumberLiteral
- [x] 377 info The statement on line 377 in class None is at the incorrect indent level: Expected one of columns [5, 9, 13] but was 3 Indentation
- [x] 381 warning The line exceeds 120 characters. The line is 168 characters. LineLength
- [x] 387 info Line ends with whitespace characters TrailingWhitespace
- [x] 389 info The closing brace for the block in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 389 info The opening brace for the block in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 390 info The statement on line 390 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 390 info The closing brace for the closure in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 391 info Code block starts with a blank line. BlockStartsWithBlankLine
- [x] 392 warning Map [mode:copy] is duplicated. DuplicateMapLiteral
- [x] 392 info Duplicate String Literal: copy DuplicateStringLiteral
- [x] 392 info The statement on line 392 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 394 info Duplicate Number Literal: 8 DuplicateNumberLiteral
- [x] 394 info The statement on line 394 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 396 info The statement on line 396 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 398 info The statement on line 398 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 399 info Duplicate String Literal: *.{log,err} DuplicateStringLiteral
- [x] 399 info The statement on line 399 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 399 info The String '*.{log,err}' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 401 info The statement on line 401 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 402 warning The line exceeds 120 characters. The line is 163 characters. LineLength
- [x] 407 info The statement on line 407 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 407 info The closing brace for the closure in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 408 info Code block starts with a blank line. BlockStartsWithBlankLine
- [x] 409 warning Map [mode:copy] is duplicated. DuplicateMapLiteral
- [x] 409 info Duplicate String Literal: copy DuplicateStringLiteral
- [x] 409 info The statement on line 409 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 410 info The statement on line 410 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 412 info The statement on line 412 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 414 info The statement on line 414 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 414 info The String '*' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 416 info The statement on line 416 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 416 info The String '
- [x] multiqc -f -s -m qualimap -o . . > multiqc.log 2> multiqc.err
- [x] ' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 417 info Line ends with whitespace characters TrailingWhitespace
- [x] 422 info Line ends with whitespace characters TrailingWhitespace
- [x] 423 info The closing brace for the block in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 423 info The if keyword within class None is not followed by a single space SpaceAfterIf
- [x] 423 info The opening brace for the block in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 424 info Code block starts with a blank line. BlockStartsWithBlankLine
- [x] 425 info The statement on line 425 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 425 info The closing brace for the closure in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 426 info The statement on line 426 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 427 warning Map [mode:copy] is duplicated. DuplicateMapLiteral
- [x] 427 info Duplicate String Literal: copy DuplicateStringLiteral
- [x] 427 info The statement on line 427 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 429 info The statement on line 429 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 431 info The statement on line 431 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 431 warning The line exceeds 120 characters. The line is 124 characters. LineLength
- [x] 433 info The statement on line 433 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 434 warning The line exceeds 120 characters. The line is 158 characters. LineLength
- [x] 438 info Line ends with whitespace characters TrailingWhitespace
- [x] 439 info The statement on line 439 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 440 warning Map [mode:copy] is duplicated. DuplicateMapLiteral
- [x] 440 info Duplicate String Literal: copy DuplicateStringLiteral
- [x] 440 info The statement on line 440 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 441 info The statement on line 441 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 443 info The statement on line 443 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 445 info The statement on line 445 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 445 info The String '*.pdf' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 447 info The statement on line 447 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 468 info The statement on line 468 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 468 info The opening brace for the closure in class None is not followed by a space or whitespace SpaceAfterOpeningBrace
- [x] 468 info The closing brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeClosingBrace
- [x] 470 info The statement on line 470 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 470 info The closing brace for the closure in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 471 warning Map [mode:copy] is duplicated. DuplicateMapLiteral
- [x] 471 info Duplicate String Literal: copy DuplicateStringLiteral
- [x] 471 info The statement on line 471 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 472 info The statement on line 472 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 474 info The statement on line 474 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 475 info The statement on line 475 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 477 info Duplicate String Literal: *.pdf DuplicateStringLiteral
- [x] 477 info The statement on line 477 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 477 info The String '*.pdf' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 480 info The statement on line 480 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 7 Indentation
- [x] 480 info The operator "/" within class None is not preceded by a space or whitespace SpaceAroundOperator
- [x] 480 info The operator "/" within class None is not followed by a space or whitespace SpaceAroundOperator
- [x] 482 info The statement on line 482 in class None is at the incorrect indent level: Expected one of columns [9, 13, 17] but was 5 Indentation
- [x] 502 info Line ends with whitespace characters TrailingWhitespace
- [x] 508 warning The line exceeds 120 characters. The line is 122 characters. LineLength
- [x] 513 warning The line exceeds 120 characters. The line is 154 characters. LineLength
- [x] 520 info The statement on line 520 in class None is at the incorrect indent level: Expected column 5 but was 3 Indentation
- [x] 520 info The closing brace for the block in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 520 info The if keyword within class None is not followed by a single space SpaceAfterIf
- [x] 520 info The opening brace for the block in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 522 info The statement on line 522 in class None is at the incorrect indent level: Expected column 9 but was 5 Indentation
- [x] 522 info The closing brace for the closure in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 523 warning Map [mode:copy] is duplicated. DuplicateMapLiteral
- [x] 523 info Duplicate String Literal: copy DuplicateStringLiteral
- [x] 523 info The statement on line 523 in class None is at the incorrect indent level: Expected one of columns [13, 17, 21] but was 7 Indentation
- [x] 524 info The statement on line 524 in class None is at the incorrect indent level: Expected one of columns [13, 17, 21] but was 7 Indentation
- [x] 526 info The statement on line 526 in class None is at the incorrect indent level: Expected one of columns [13, 17, 21] but was 9 Indentation
- [x] 526 info Line ends with whitespace characters TrailingWhitespace
- [x] 528 info The statement on line 528 in class None is at the incorrect indent level: Expected one of columns [13, 17, 21] but was 9 Indentation
- [x] 528 info The String '*.stats' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 529 info Duplicate String Literal: *.err DuplicateStringLiteral
- [x] 529 info The statement on line 529 in class None is at the incorrect indent level: Expected one of columns [13, 17, 21] but was 9 Indentation
- [x] 529 info The String '*.err' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 531 info The statement on line 531 in class None is at the incorrect indent level: Expected one of columns [13, 17, 21] but was 9 Indentation
- [x] 537 info The statement on line 537 in class None is at the incorrect indent level: Expected column 9 but was 5 Indentation
- [x] 537 info The closing brace for the closure in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 538 info The statement on line 538 in class None is at the incorrect indent level: Expected one of columns [13, 17, 21] but was 7 Indentation
- [x] 540 info The statement on line 540 in class None is at the incorrect indent level: Expected one of columns [13, 17, 21] but was 9 Indentation
- [x] 542 info The statement on line 542 in class None is at the incorrect indent level: Expected one of columns [13, 17, 21] but was 9 Indentation
- [x] 544 info The statement on line 544 in class None is at the incorrect indent level: Expected one of columns [13, 17, 21] but was 9 Indentation
- [x] 550 info The statement on line 550 in class None is at the incorrect indent level: Expected column 9 but was 5 Indentation
- [x] 550 info The closing brace for the closure in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 551 info The statement on line 551 in class None is at the incorrect indent level: Expected one of columns [13, 17, 21] but was 7 Indentation
- [x] 553 info The statement on line 553 in class None is at the incorrect indent level: Expected one of columns [13, 17, 21] but was 9 Indentation
- [x] 555 info The statement on line 555 in class None is at the incorrect indent level: Expected one of columns [13, 17, 21] but was 9 Indentation
- [x] 557 info The statement on line 557 in class None is at the incorrect indent level: Expected one of columns [13, 17, 21] but was 9 Indentation
- [x] 562 info The statement on line 562 in class None is at the incorrect indent level: Expected column 9 but was 5 Indentation
- [x] 562 info The if keyword within class None is not followed by a single space SpaceAfterIf
- [x] 562 info The opening brace for the block in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 564 info The statement on line 564 in class None is at the incorrect indent level: Expected column 13 but was 7 Indentation
- [x] 565 info The statement on line 565 in class None is at the incorrect indent level: Expected column 13 but was 7 Indentation
- [x] 565 info The closing brace for the closure in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 566 info The statement on line 566 in class None is at the incorrect indent level: Expected one of columns [17, 21, 25] but was 9 Indentation
- [x] 568 info The statement on line 568 in class None is at the incorrect indent level: Expected one of columns [17, 21, 25] but was 11 Indentation
- [x] 570 info The statement on line 570 in class None is at the incorrect indent level: Expected one of columns [17, 21, 25] but was 11 Indentation
- [x] 572 info The statement on line 572 in class None is at the incorrect indent level: Expected one of columns [17, 21, 25] but was 11 Indentation
- [x] 576 info The closing brace for the block in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 577 info The statement on line 577 in class None is at the incorrect indent level: Expected column 13 but was 7 Indentation
- [x] 577 info Line ends with whitespace characters TrailingWhitespace
- [x] 577 info The String '0' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 583 info Duplicate Number Literal: 0 DuplicateNumberLiteral
- [x] 583 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 583 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 583 info The statement on line 583 in class None is at the incorrect indent level: Expected column 9 but was 3 Indentation
- [x] 583 info The opening brace for the closure in class None is not followed by a space or whitespace SpaceAfterOpeningBrace
- [x] 583 info The closing brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeClosingBrace
- [x] 583 info The opening brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 584 info Duplicate Number Literal: 0 DuplicateNumberLiteral
- [x] 584 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 584 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 584 info The statement on line 584 in class None is at the incorrect indent level: Expected column 9 but was 3 Indentation
- [x] 584 info The opening brace for the closure in class None is not followed by a space or whitespace SpaceAfterOpeningBrace
- [x] 584 info The closing brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeClosingBrace
- [x] 584 info The opening brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 585 info Duplicate Number Literal: 0 DuplicateNumberLiteral
- [x] 585 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 585 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 585 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 585 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 585 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 585 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 585 info The statement on line 585 in class None is at the incorrect indent level: Expected column 9 but was 3 Indentation
- [x] 585 warning The line exceeds 120 characters. The line is 169 characters. LineLength
- [x] 585 info The opening brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 586 info Line ends with whitespace characters TrailingWhitespace
- [x] 588 info The statement on line 588 in class None is at the incorrect indent level: Expected column 9 but was 3 Indentation
- [x] 588 info The closing brace for the closure in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 588 info Line ends with whitespace characters TrailingWhitespace
- [x] 589 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 589 info The statement on line 589 in class None is at the incorrect indent level: Expected column 13 but was 5 Indentation
- [x] 590 info The statement on line 590 in class None is at the incorrect indent level: Expected column 13 but was 5 Indentation
- [x] 590 warning The instanceof operator is used in class None Instanceof
- [x] 590 info The closing brace for the block in class None is not followed by a space or whitespace SpaceAfterClosingBrace
- [x] 591 info The statement on line 591 in class None is at the incorrect indent level: Expected column 17 but was 7 Indentation
- [x] 591 info The String '%,.0f' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 591 info Semicolons as line endings can be removed safely UnnecessarySemicolon
- [x] 592 info The opening brace for the block in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 593 info The statement on line 593 in class None is at the incorrect indent level: Expected column 17 but was 7 Indentation
- [x] 593 info The String '%,d' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 593 info Semicolons as line endings can be removed safely UnnecessarySemicolon
- [x] 594 info Line ends with whitespace characters TrailingWhitespace
- [x] 597 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 597 info The statement on line 597 in class None is at the incorrect indent level: Expected column 9 but was 3 Indentation
- [x] 597 info The opening brace for the closure in class None is not followed by a space or whitespace SpaceAfterOpeningBrace
- [x] 597 info The closing brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeClosingBrace
- [x] 597 info The opening brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 597 info The opening brace for the closure in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 597 info Line ends with whitespace characters TrailingWhitespace
- [x] 598 info The statement on line 598 in class None is at the incorrect indent level: Depending on your chaining style, expected one of [13, 17, 21] or one of [92, 96, 100] columns, but was 5 Indentation
- [x] 601 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 601 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 602 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 603 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 603 info Line ends with whitespace characters TrailingWhitespace
- [x] 604 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 604 info Semicolons as line endings can be removed safely UnnecessarySemicolon
- [x] 605 info Duplicate Number Literal: 0 DuplicateNumberLiteral
- [x] 605 info Duplicate Number Literal: 0 DuplicateNumberLiteral
- [x] 605 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 605 info The statement on line 605 in class None is at the incorrect indent level: Depending on your chaining style, expected one of [13, 17, 21] or one of [92, 96, 100] columns, but was 5 Indentation
- [x] 605 info The if keyword within class None is not followed by a single space SpaceAfterIf
- [x] 605 info The opening brace for the block in class None is not preceded by a space or whitespace SpaceBeforeOpeningBrace
- [x] 606 info The statement on line 606 in class None is at the incorrect indent level: Expected column 17 but was 5 Indentation
- [x] 607 info Duplicate Number Literal: 0 DuplicateNumberLiteral
- [x] 607 info Duplicate Number Literal: 0 DuplicateNumberLiteral
- [x] 607 info Duplicate Number Literal: 5 DuplicateNumberLiteral
- [x] 607 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 607 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 607 info By convention closure parameters should be specified explicitly. ImplicitClosureParameter
- [x] 607 info The parameter ((it[0] / it[5]) * 100.0) in the call to method format within class None is not preceded by a space or whitespace SpaceAfterComma
- [x] 607 info The String '%.2f' can be wrapped in single quotes instead of double quotes UnnecessaryGString
- [x] 608 info Semicolons as line endings can be removed safely UnnecessarySemicolon
- [x] 610 info The statement on line 610 in class None is at the incorrect indent level: Depending on your chaining style, expected one of [13, 17, 21] or one of [92, 96, 100] columns, but was 5 Indentation
- [x] 613 info The statement on line 613 in class None is at the incorrect indent level: Expected column 9 but was 3 IndentationRaphael Müllerraphael.mueller@computational.bio.uni-giessen.deRaphael Müllerraphael.mueller@computational.bio.uni-giessen.de