diff --git a/software/bandage/image/functions.nf b/software/bandage/image/functions.nf new file mode 100644 index 00000000..d25eea86 --- /dev/null +++ b/software/bandage/image/functions.nf @@ -0,0 +1,59 @@ +/* + * ----------------------------------------------------- + * Utility functions used in nf-core DSL2 module files + * ----------------------------------------------------- + */ + +/* + * Extract name of software tool from process name using $task.process + */ +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +/* + * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules + */ +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.publish_by_id = args.publish_by_id ?: false + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +/* + * Tidy up and join elements of a list to return a path string + */ +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +/* + * Function to save/publish module results + */ +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_id) { + path_list.add(args.publish_id) + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" + } + } +} diff --git a/software/bandage/image/main.nf b/software/bandage/image/main.nf new file mode 100644 index 00000000..95b9154c --- /dev/null +++ b/software/bandage/image/main.nf @@ -0,0 +1,38 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +def options = initOptions(params.options) + +process BANDAGE_IMAGE { + tag "${meta.id}" + label 'process_low' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + conda (params.enable_conda ? 'bioconda::bandage=0.8.1' : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/bandage:0.8.1--hc9558a2_2" + } else { + container "quay.io/biocontainers/bandage:0.8.1--hc9558a2_2" + } + + input: + tuple val(meta), path(gfa) + + output: + tuple val(meta), path('*.png'), emit: png + tuple val(meta), path('*.svg'), emit: svg + path '*.version.txt' , emit: version + + script: + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + """ + Bandage image $gfa ${prefix}.png $options.args + Bandage image $gfa ${prefix}.svg $options.args + + echo \$(Bandage --version 2>&1) | sed 's/^.*Version: //; s/ .*\$//' > ${software}.version.txt + """ +} diff --git a/software/bandage/image/meta.yml b/software/bandage/image/meta.yml new file mode 100644 index 00000000..85de09a2 --- /dev/null +++ b/software/bandage/image/meta.yml @@ -0,0 +1,64 @@ +name: bandage_image +description: Render an assembly graph in GFA 1.0 format to PNG and SVG image formats +keywords: + - gfa + - graph + - assembly + - visualisation +tools: + - bandage: + description: | + Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily + homepage: https://github.com/rrwick/Bandage + documentation: https://github.com/rrwick/Bandage +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$params.outdir/` + - publish_dir_mode: + type: string + description: | + Value for the Nextflow `publishDir` mode parameter. + Available: symlink, rellink, link, copy, copyNoFollow, move. + - enable_conda: + type: boolean + description: | + Run the module with Conda using the software specified + via the `conda` directive + - singularity_pull_docker_container: + type: boolean + description: | + Instead of directly downloading Singularity images for use with Singularity, + force the workflow to pull and convert Docker containers instead. +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gfa: + type: file + description: Assembly graph in GFA 1.0 format + pattern: "*.gfa" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - png: + type: file + description: Bandage image in PNG format + pattern: "*.png" + - svg: + type: file + description: Bandage image in SVG format + pattern: "*.svg" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" +authors: + - "@heuermh" diff --git a/tests/data/gfa/B-3106.gfa b/tests/data/gfa/B-3106.gfa new file mode 100644 index 00000000..e2467654 --- /dev/null +++ b/tests/data/gfa/B-3106.gfa @@ -0,0 +1,1438 @@ +H VN:Z:1.0 +S 1 AT +S 2 TCTGGAA +S 3 G +S 4 GTTCTCAGGTCTTTATTTGCTCT +S 5 C +S 6 TCA +S 7 A +S 8 ATTCCAGGAATTGACTTATTTAATTAATCCATCAACCTCTCATAGCAAATATTTGAGAAAACAAATTTATATTCAGATTCTTATTTTCAGTAGGGAAGTAAGAAGTTGCAGCTCAGTGCAC +S 9 G +S 10 TAAAGTTGAGACAGAGATGGAGACATCCAGCCCCACC +S 11 T +S 12 CTCTGGAACA +S 13 A +S 14 GAAAGATGACTGGGGAGGAAACACA +S 15 G +S 16 G +S 17 TCAGCATGGGAACAGGGGTCAC +S 18 A +S 19 GTGGACAC +S 20 A +S 21 A +S 22 G +S 23 G +S 24 G +S 25 TG +S 26 G +S 27 GCTGTCTCTCCACCTCCTCACATTATGCTAACAGGGAC +S 28 G +S 29 CAGACACATTCAGGTGCCTTTGCAGAAAGAGATGCCAGAGGCTCTTGAAGTCACAAAGGGGAGG +S 30 C +S 31 GTGAAGAAATCCTGCATCTC +S 32 A +S 33 GTCCCTCACAAGACAGCTGTCTCAGGCTACAGAAAACAACAGTCATGAACAAATTCTGGTTAGTCATGGTAAG +S 34 C +S 35 GATGACACTCT +S 36 A +S 37 AACAGCCCAC +S 38 C +S 39 ACACACGCGAAACATCCCAATCAAAGAAT +S 40 C +S 41 C +S 42 CCATT +S 43 A +S 44 CCCAGGCCTTTCCCC +S 45 T +S 46 CTG +S 47 C +S 48 A +S 49 A +S 50 AGA +S 51 G +S 52 A +S 53 A +S 54 CACTCTAGACCCCAAGAATCTCACCTTTTCAAGCTGTGAGAGACACATCAGAGCCCTGGGCACTGTCGCTG +S 55 C +S 56 CTGGAGTAGAACAAAAACAGGACCTGGTCAGAGCCCGCAGGAGACGTGGGACAGGAGGAATTATGGGGTGGGTGAGCTCCTCCACACTCCC +S 57 A +S 58 CCCCCA +S 59 C +S 60 CACTTACACGCAGCCTGAGAGTAGCTCCCTCCTTTTCCACCTGTGGGAAGAAAATG +S 61 T +S 62 CCTGTGAGGG +S 63 C +S 64 ACTGGGAGGAAGCAGG +S 65 G +S 66 CCATGAGATCTTAGAGGAACCTCCT +S 67 A +S 68 GTCTTGGA +S 69 C +S 70 CCAAAAGGAATTTCCAGAAGTATGACTACAGACCCA +S 71 G +S 72 GGCAGGATCAGGAAACACGAGGAAAGCAAGTGTGGGTCCTGGACCAACTGCCCTCCTAAGGTCTGTCCTTAGCAGGGACCTTCCCCTGACTCATGAATGCTG +S 73 G +S 74 AATCAGGACCCCAACACCACAACCA +S 75 T +S 76 CAAGG +S 77 T +S 78 GATACATC +S 79 C +S 80 A +S 81 T +S 82 C +S 83 CTTCATTGTCACATGTGCTGCACAAAAGAGTAAGTGCTGGCACACAGGGTCCCAG +S 84 G +S 85 CTG +S 86 C +S 87 G +S 88 TTAGCCCCTGTGTG +S 89 C +S 90 ATGCTGC +S 91 T +S 92 TCCCAGTAATGAGGCAGGGAACACTTCTACCTGGGGCTTGAAACCCCCAGTGGGACAAGAAAACCCAGACCCCACCCCTCACCCCTTCCCTACCTGA +S 93 A +S 94 CTCTTCCTCCTACACATCACAG +S 95 C +S 96 AGCGACCACAGCTCCGATGACCACAACTGCTAGGACAGCCAGGCCAGCAACAATGCCCACGATGGGGA +S 97 C +S 98 GGTGGACTGGGAAGA +S 99 C +S 100 GGCTCTGGGAAAGGA +S 101 G +S 102 GGGAAGA +S 103 T +S 104 GAGGGGCCCTGACCCTGCT +S 105 GAAGGGCTCC +S 106 TGCTTTCCCTGAGAA +S 107 G +S 108 AGATATGACCCCTCATCCCCCTCCTTACCCCATCTCAGGGTGAGGGGCTTCGGCAGCCCCTCATGCTGTACATGGCATGTGTATCTCTGCTCTTCTCCAGAAGGCACCACCACAGCTGCCCACTTCTGGAAGGTTCTATCTCCTGCTGGTCTGGTCTCCACAAGCTC +S 109 A +S 110 GTGTCCTGAGTTTGGTCCTCGCCATCCCGCTGCCAGGTCAGTGTGATCTCCGCAGGGTAGAA +S 111 A +S 112 CCCAGGGCCCAGCACCTCAGGGTG +S 113 G +S 114 CCTCATGGTCAGAGATGGGGTGGTGGGTCAC +S 115 G +S 116 TGTGTCTTTGGGGGGTCTGATGGGAAGAGTCAGAAAATTCAGGCGCTTTGCATCT +S 117 T +S 118 TCAT +S 119 G +S 120 G +S 121 G +S 122 ACACCCTAGGACCACCCATGTGACCAGCCTGAGAATGGACAGGACACCTGGGGTGGGGAAGGGGCACAGAACCCAGACACCAGC +S 123 CT +S 124 GGA +S 125 C +S 126 GCAGGCACCTGGGATAAT +S 127 CTC +S 128 CTATTCATTGGAAAGTTCGAGTCTCTGAGCGGGGAACAG +S 129 G +S 130 GACTTCTGCTCCTGATCTGAGTGGAGGTAAAGTGACTCAGAAGTGCTGGAATCAGAGCCCCAAACACACTGAGTGTGAGGCAGAGAACAAGGCCTGAGAGGAAAAGTCA +S 131 C +S 132 GGTTCCCAAGGCTGCTGCAGGGGTCAAAG +S 133 G +S 134 GGACCCCTGATCA +S 135 G +S 136 TAT +S 137 T +S 138 CTAGGGACTGTCTTCCCCTCCATTTCCTCAGAGACGTCAT +S 139 T +S 140 CCTTAATTGT +S 141 C +S 142 TAGAGAGAAGAGGGGGCCCTCAGAGGAAACTCAGGAAAACTCATGCCATTCTCCATTCAA +S 143 C +S 144 GGAGGGCGACATTCTAGCGCTGATCCCATTTTCCTCCTCTTCTCGTGGGAGGCCATCCCCGGCGACCTATAGGAGATGGGGAAGGCTCCCCACTGCCCCTGGTACC +S 145 A +S 146 GCGCGCT +S 147 C +S 148 CAGC +S 149 T +S 150 T +S 151 G +S 152 TCCTTCCCGTTCTCCAGGT +S 153 A +S 154 TCTGCGGAGC +S 155 C +S 156 ACTCCACGCAC +S 157 TC +S 158 GCCCTCCAGGTAGGCTCT +S 159 C +S 160 C +S 161 G +S 162 CTGCTCCGCC +S 163 T +S 164 CACGGGCCGCCTCCCACTTGCGCTGGGTGATCTGAGCCGC +S 165 C +S 166 GTGTCCGC +S 167 G +S 168 GCGGTCCAGGAGC +S 169 G +S 170 CAG +S 171 G +S 172 TCCTCGTTCAGGGCGATGTAATCCTTGCCGTCGTAGGCG +S 173 T +S 174 A +S 175 CTGGT +S 176 C +S 177 AT +S 178 G +S 179 CCCGCGGAGGAGGCGCCCGTC +S 180 C +S 181 GGCCCCACGTCGCAGCC +S 182 G +S 183 T +S 184 ACAT +S 185 G +S 186 CTCTGGA +S 187 G +S 188 G +S 189 G +S 190 TGTGAGACCCTGGCCC +S 191 C +S 192 G +S 193 G +S 194 CCCCGCGGTCAGCCC +S 195 A +S 196 GT +S 197 C +S 198 GAGCCCCGCCCCGCCCCGACCAACCCGCGGGGATTTTGGCCTCAACTGAAAATGAAACCGGGTAAACGCGCCTGGGGCTCTCGCCGGTCGAGGGT +S 199 C +S 200 TGGGCGGGTCCCGCGGCCTC +S 201 A +S 202 G +S 203 A +S 204 GGCGGATCTCGGACCCGGAGACTCGGGGCGACCCGGGCCGT +S 205 A +S 206 CGTGGGGGATGGGGAGTCGTGACCTGCGCCCC +S 207 G +S 208 GGCCGGGGTCACTCACCGGCCTCGCTCTGGTTGTAGTAGC +S 209 C +S 210 G +S 211 C +S 212 GC +S 213 AG +S 214 G +S 215 T +S 216 T +S 217 C +S 218 CGCAGG +S 219 C +S 220 T +S 221 CTCTCGGT +S 222 C +S 223 AGTCTGTG +S 224 CC +S 225 T +S 226 G +S 227 GG +S 228 C +S 229 CTTG +S 230 T +S 231 AGATCTGTGT +S 232 G +S 233 T +S 234 T +S 235 CCGGTCCCAATACTCCGGCCCCTC +S 236 C +S 237 TGCTCTATCCA +S 238 C +S 239 GGCGCCCG +S 240 C +S 241 GGC +S 242 T +S 243 CC +S 244 T +S 245 C +S 246 T +S 247 CTCGGACTCG +S 248 C +S 249 GGCGTCGCTGTCGAACCTCACGAAC +S 250 T +S 251 G +S 252 G +S 253 GTG +S 254 T +S 255 CGTCCACGTAGCCCAC +S 256 T +S 257 G +S 258 A +S 259 GATGAAGCGGGGCTCCCCGCGGCCGGGCCGGGACA +S 260 C +S 261 GG +S 262 A +S 263 GGTGT +S 264 A +S 265 GAAATACCTCATGGAGTGGGAGCCT +S 266 G +S 267 GGGG +S 268 T +S 269 G +S 270 AGGAGGGGCTGAGACCCGCC +S 271 C +S 272 GACCCTCCTCCCGGCGCGGCTCC +S 273 T +S 274 C +S 275 A +S 276 GGTCCTGCGCCCCCGCCTGCGGTCCCCTC +S 277 G +S 278 CTCCTCCC +S 279 GG +S 280 CAGAGGCCATTTCCCT +S 281 C +S 282 CCGA +S 283 CCCGCACTCACC +S 284 G +S 285 GCCCAGGTCTCGGTCAGGGCCA +S 286 GG +S 287 GC +S 288 C +S 289 G +S 290 CC +S 291 G +S 292 AGAGCAGCAGGAGGA +S 293 C +S 294 GGTTCGGGG +S 295 C +S 296 GCC +S 297 A +S 298 TGACC +S 299 A +S 300 GCATCTCGG +S 301 C +S 302 GTCTGAGGA +S 303 GA +S 304 C +S 305 T +S 306 C +S 307 TGAGTCCGGGTGGGTGCGTGGGGACTTTAGAAC +S 308 T +S 309 T +S 310 A +S 311 T +S 312 C +S 313 G +S 314 C +S 315 A +S 316 C +S 317 G +S 318 G +S 319 A +S 320 G +S 321 G +S 322 C +S 323 C +S 324 T +S 325 C +S 326 G +S 327 C +S 328 G +S 329 GT +S 330 GTC +S 331 A +S 332 G +S 333 C +S 334 T +S 335 C +S 336 C +S 337 TG +S 338 T +S 339 T +S 340 A +S 341 C +S 342 T +S 343 C +S 344 C +S 345 C +S 346 A +S 347 G +S 348 A +S 349 G +S 350 GG +S 351 T +S 352 G +S 353 A +S 354 G +S 355 A +S 356 A +S 357 G +S 358 C +S 359 G +S 360 AG +S 361 A +S 362 T +S 363 C +S 364 A +S 365 C +S 366 T +S 367 A +S 368 G +S 369 A +S 370 GC +S 371 G +S 372 G +S 373 T +S 374 A +S 375 G +S 376 C +S 377 C +S 378 T +S 379 T +S 380 A +S 381 G +S 382 T +S 383 C +S 384 G +S 385 T +S 386 CA +S 387 C +S 388 CT +S 389 C +S 390 C +S 391 G +S 392 G +S 393 C +S 394 T +S 395 T +S 396 A +S 397 G +S 398 G +S 399 G +S 400 G +S 401 A +S 402 A +S 403 C +S 404 T +S 405 T +S 406 T +S 407 T 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addParams( options: [:] ) + +workflow test_bandage_image { + + def input = [] + input = [ [ id:'B-3106' ], // meta map + [ file("${launchDir}/tests/data/gfa/B-3106.gfa", checkIfExists: true) ] ] + + BANDAGE_IMAGE ( input ) +} diff --git a/tests/software/bandage/image/test.yml b/tests/software/bandage/image/test.yml new file mode 100644 index 00000000..c6bd80af --- /dev/null +++ b/tests/software/bandage/image/test.yml @@ -0,0 +1,10 @@ +- name: bandage image + command: nextflow run ./tests/software/bandage/image -entry test_bandage_image -c tests/config/nextflow.config + tags: + - bandage + - bandage_image + files: + - path: output/bandage/B-3106.png + should_exist: true + - path: output/bandage/B-3106.svg + should_exist: true