Mercurial > repos > kkonganti > cfsan_centriflaken

annotate 0.2.1/workflows/centriflaken.nf @ 47:30191f39a957

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"planemo upload"
author kkonganti
date Mon, 11 Jul 2022 12:19:48 -0400
parents 77494b0fa3c7
children
rev   line source
kkonganti@0 1 // Define any required imports for this specific workflow
kkonganti@0 2 import java.nio.file.Paths
kkonganti@0 3 import nextflow.file.FileHelper
kkonganti@0 4
kkonganti@0 5 // Include any necessary methods
kkonganti@0 6 include { \
kkonganti@0 7 summaryOfParams; stopNow; fastqEntryPointHelp; sendMail; \
kkonganti@0 8 addPadding; wrapUpHelp } from "${params.routines}"
kkonganti@0 9 include { kraken2Help } from "${params.toolshelp}${params.fs}kraken2"
kkonganti@0 10 include { centrifugeHelp } from "${params.toolshelp}${params.fs}centrifuge"
kkonganti@0 11 include { flyeHelp } from "${params.toolshelp}${params.fs}flye"
kkonganti@0 12 include { serotypefinderHelp } from "${params.toolshelp}${params.fs}serotypefinder"
kkonganti@0 13 include { seqsero2Help } from "${params.toolshelp}${params.fs}seqsero2"
kkonganti@0 14 include { mlstHelp } from "${params.toolshelp}${params.fs}mlst"
kkonganti@0 15 include { abricateHelp } from "${params.toolshelp}${params.fs}abricate"
kkonganti@0 16
kkonganti@0 17 // Exit if help requested before any subworkflows
kkonganti@0 18 if (params.help) {
kkonganti@0 19 log.info help()
kkonganti@0 20 exit 0
kkonganti@0 21 }
kkonganti@0 22
kkonganti@0 23 // Include any necessary modules and subworkflows
kkonganti@0 24 include { PROCESS_FASTQ } from "${params.subworkflows}${params.fs}process_fastq"
kkonganti@0 25 include { FASTQC } from "${params.modules}${params.fs}fastqc${params.fs}main"
kkonganti@0 26 include { CENTRIFUGE_CLASSIFY } from "${params.modules}${params.fs}centrifuge${params.fs}classify${params.fs}main"
kkonganti@0 27 include { CENTRIFUGE_PROCESS } from "${params.modules}${params.fs}centrifuge${params.fs}process${params.fs}main"
kkonganti@0 28 include { SEQKIT_GREP } from "${params.modules}${params.fs}seqkit${params.fs}grep${params.fs}main"
kkonganti@0 29 include { FLYE_ASSEMBLE } from "${params.modules}${params.fs}flye${params.fs}assemble${params.fs}main"
kkonganti@0 30 include { KRAKEN2_CLASSIFY } from "${params.modules}${params.fs}kraken2${params.fs}classify${params.fs}main"
kkonganti@0 31 include { KRAKEN2_EXTRACT_CONTIGS } from "${params.modules}${params.fs}kraken2${params.fs}extract_contigs${params.fs}main"
kkonganti@0 32 include { SEROTYPEFINDER } from "${params.modules}${params.fs}serotypefinder${params.fs}main"
kkonganti@0 33 include { SEQSERO2 } from "${params.modules}${params.fs}seqsero2${params.fs}main"
kkonganti@0 34 include { MLST } from "${params.modules}${params.fs}mlst${params.fs}main"
kkonganti@0 35 include { ABRICATE_RUN } from "${params.modules}${params.fs}abricate${params.fs}run${params.fs}main"
kkonganti@0 36 include { ABRICATE_SUMMARY } from "${params.modules}${params.fs}abricate${params.fs}summary${params.fs}main"
kkonganti@0 37 include { TABLE_SUMMARY } from "${params.modules}${params.fs}cat${params.fs}tables${params.fs}main"
kkonganti@0 38 include { MULTIQC } from "${params.modules}${params.fs}multiqc${params.fs}main"
kkonganti@0 39 include { DUMP_SOFTWARE_VERSIONS } from "${params.modules}${params.fs}custom${params.fs}dump_software_versions${params.fs}main"
kkonganti@0 40
kkonganti@0 41
kkonganti@0 42
kkonganti@0 43 /*
kkonganti@0 44 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0 45 INPUTS AND ANY CHECKS FOR THE CENTRIFLAKEN WORKFLOW
kkonganti@0 46 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0 47 */
kkonganti@0 48
kkonganti@0 49 def kraken2_db_dir = file ( "${params.kraken2_db}" )
kkonganti@0 50 def centrifuge_x = file ( "${params.centrifuge_x}" )
kkonganti@0 51 def reads_platform = 0
kkonganti@0 52 def abricate_dbs = [ 'ncbiamrplus', 'resfinder', 'megares', 'argannot' ]
kkonganti@0 53
kkonganti@0 54 reads_platform += (params.flye_nano_raw ? 1 : 0)
kkonganti@0 55 reads_platform += (params.flye_nano_corr ? 1 : 0)
kkonganti@0 56 reads_platform += (params.flye_nano_hq ? 1 : 0)
kkonganti@0 57 reads_platform += (params.flye_pacbio_raw ? 1 : 0)
kkonganti@0 58 reads_platform += (params.flye_pacbio_corr ? 1 : 0)
kkonganti@0 59 reads_platform += (params.flye_pacbio_hifi ? 1 : 0)
kkonganti@0 60
kkonganti@0 61 if (!kraken2_db_dir.exists() || !centrifuge_x.getParent().exists()) {
kkonganti@0 62 stopNow("Please check if the following absolute paths are valid:\n" +
kkonganti@0 63 "${params.kraken2_db}\n${params.centrifuge_x}\n" +
kkonganti@0 64 "Cannot proceed further!")
kkonganti@0 65 }
kkonganti@0 66
kkonganti@0 67 if (reads_platform > 1 || reads_platform == 0) {
kkonganti@0 68 msg_0 = (reads_platform > 1 ? "only" : "at least")
kkonganti@0 69 stopNow("Please mention ${msg_0} one read platform for use with the flye assembler\n" +
kkonganti@0 70 "using any one of the following options:\n" +
kkonganti@0 71 "--flye_nano_raw\n--flye_nano_corr\n--flye_nano_hq\n" +
kkonganti@0 72 "--flye_pacbio_raw\n--flye_pacbio_corr\n--flye_pacbio_hifi")
kkonganti@0 73 }
kkonganti@0 74
kkonganti@0 75 if (params.centrifuge_extract_bug != params.kraken2_extract_bug) {
kkonganti@0 76 stopNow("Please make sure that the bug to be extracted is same\n" +
kkonganti@0 77 "for both --centrifuge_extract_bug and --kraken2_extract_bug options.")
kkonganti@0 78 }
kkonganti@0 79
kkonganti@0 80 /*
kkonganti@0 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0 82 RUN THE CENTRIFLAKEN WORKFLOW
kkonganti@0 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0 84 */
kkonganti@0 85
kkonganti@0 86 workflow CENTRIFLAKEN {
kkonganti@0 87 main:
kkonganti@0 88 ch_asm_filtered_contigs = Channel.empty()
kkonganti@0 89 ch_mqc_custom_tbl = Channel.empty()
kkonganti@0 90
kkonganti@0 91 log.info summaryOfParams()
kkonganti@0 92
kkonganti@0 93 PROCESS_FASTQ()
kkonganti@0 94 .processed_reads
kkonganti@0 95 .map {
kkonganti@0 96 meta, fastq ->
kkonganti@0 97 meta.centrifuge_x = params.centrifuge_x
kkonganti@0 98 meta.kraken2_db = params.kraken2_db
kkonganti@0 99 [meta, fastq]
kkonganti@0 100 }
kkonganti@0 101 .set { ch_processed_reads }
kkonganti@0 102
kkonganti@0 103 PROCESS_FASTQ
kkonganti@0 104 .out
kkonganti@0 105 .versions
kkonganti@0 106 .set { software_versions }
kkonganti@0 107
kkonganti@0 108 FASTQC ( ch_processed_reads )
kkonganti@0 109
kkonganti@47 110 CENTRIFUGE_CLASSIFY ( ch_processed_reads )
kkonganti@0 111
kkonganti@47 112 CENTRIFUGE_PROCESS (
kkonganti@0 113 CENTRIFUGE_CLASSIFY.out.report
kkonganti@0 114 .join( CENTRIFUGE_CLASSIFY.out.output )
kkonganti@0 115 )
kkonganti@0 116
kkonganti@47 117 ch_processed_reads.join ( CENTRIFUGE_PROCESS.out.extracted )
kkonganti@0 118 .set { ch_centrifuge_extracted }
kkonganti@0 119
kkonganti@0 120 SEQKIT_GREP ( ch_centrifuge_extracted )
kkonganti@0 121
kkonganti@0 122 FLYE_ASSEMBLE ( SEQKIT_GREP.out.fastx )
kkonganti@0 123
kkonganti@0 124 FLYE_ASSEMBLE
kkonganti@0 125 .out
kkonganti@0 126 .assembly
kkonganti@0 127 .set { ch_flye_assembly }
kkonganti@0 128
kkonganti@0 129 ch_flye_assembly.ifEmpty { [ false, false ] }
kkonganti@0 130
kkonganti@47 131 KRAKEN2_CLASSIFY ( ch_flye_assembly )
kkonganti@0 132
kkonganti@0 133 KRAKEN2_EXTRACT_CONTIGS (
kkonganti@0 134 ch_flye_assembly
kkonganti@0 135 .join( KRAKEN2_CLASSIFY.out.kraken_output ),
kkonganti@0 136 params.kraken2_extract_bug
kkonganti@0 137 )
kkonganti@0 138
kkonganti@0 139 KRAKEN2_EXTRACT_CONTIGS
kkonganti@0 140 .out
kkonganti@0 141 .asm_filtered_contigs
kkonganti@0 142 .map {
kkonganti@0 143 meta, fastq ->
kkonganti@0 144 meta.organism = params.kraken2_extract_bug.split(/\s+/)[0].capitalize()
kkonganti@0 145 meta.serotypefinder_db = params.serotypefinder_db
kkonganti@0 146 [meta, fastq]
kkonganti@0 147 }
kkonganti@0 148 .set { ch_asm_filtered_contigs }
kkonganti@0 149
kkonganti@0 150 SEROTYPEFINDER ( ch_asm_filtered_contigs )
kkonganti@0 151
kkonganti@0 152 SEQSERO2 ( ch_asm_filtered_contigs )
kkonganti@0 153
kkonganti@0 154 MLST ( ch_asm_filtered_contigs )
kkonganti@0 155
kkonganti@0 156 ABRICATE_RUN (
kkonganti@0 157 ch_asm_filtered_contigs,
kkonganti@0 158 abricate_dbs
kkonganti@0 159 )
kkonganti@0 160
kkonganti@0 161 ABRICATE_RUN
kkonganti@0 162 .out
kkonganti@0 163 .abricated
kkonganti@0 164 .map { meta, abres -> [ abricate_dbs, abres ] }
kkonganti@0 165 .groupTuple(by: [0])
kkonganti@0 166 .map { it -> tuple ( it[0], it[1].flatten() ) }
kkonganti@0 167 .set { ch_abricated }
kkonganti@0 168
kkonganti@0 169 ABRICATE_SUMMARY ( ch_abricated )
kkonganti@0 170
kkonganti@0 171 // ABRICATE_SUMMARY.out.ecoli_vf.set { ch_abricate_summary_ecoli_vf }
kkonganti@0 172 // ch_abricate_summary_ecoli_vf.ifEmpty { [ false, false ] }
kkonganti@0 173
kkonganti@0 174 CENTRIFUGE_CLASSIFY.out.kreport
kkonganti@0 175 .map { meta, kreport -> [ kreport ] }
kkonganti@0 176 .flatten()
kkonganti@0 177 .concat (
kkonganti@0 178 KRAKEN2_CLASSIFY.out.kraken_report
kkonganti@0 179 .map { meta, kreport -> [ kreport ] }
kkonganti@0 180 .flatten(),
kkonganti@0 181 FASTQC.out.zip
kkonganti@0 182 .map { meta, zip -> [ zip ] }
kkonganti@0 183 .flatten()
kkonganti@0 184 )
kkonganti@0 185 .set { ch_mqc_classify }
kkonganti@0 186
kkonganti@0 187 if (params.serotypefinder_run) {
kkonganti@0 188 SEROTYPEFINDER
kkonganti@0 189 .out
kkonganti@0 190 .serotyped
kkonganti@0 191 .map { meta, tsv -> [ 'serotypefinder', tsv ] }
kkonganti@0 192 .groupTuple(by: [0])
kkonganti@0 193 .map { it -> tuple ( it[0], it[1].flatten() ) }
kkonganti@0 194 .set { ch_mqc_custom_tbl }
kkonganti@0 195 } else if (params.seqsero2_run) {
kkonganti@0 196 SEQSERO2
kkonganti@0 197 .out
kkonganti@0 198 .serotyped
kkonganti@0 199 .map { meta, tsv -> [ 'seqsero2', tsv ] }
kkonganti@0 200 .groupTuple(by: [0])
kkonganti@0 201 .map { it -> tuple ( it[0], it[1].flatten() ) }
kkonganti@0 202 .set { ch_mqc_custom_tbl }
kkonganti@0 203 }
kkonganti@0 204
kkonganti@0 205 ch_mqc_custom_tbl
kkonganti@0 206 .concat (
kkonganti@0 207 ABRICATE_SUMMARY.out.ncbiamrplus.map{ it -> tuple ( it[0], it[1] )},
kkonganti@0 208 ABRICATE_SUMMARY.out.resfinder.map{ it -> tuple ( it[0], it[1] )},
kkonganti@0 209 ABRICATE_SUMMARY.out.megares.map{ it -> tuple ( it[0], it[1] )},
kkonganti@0 210 ABRICATE_SUMMARY.out.argannot.map{ it -> tuple ( it[0], it[1] )},
kkonganti@0 211 )
kkonganti@0 212 .groupTuple(by: [0])
kkonganti@0 213 .map { it -> [ it[0], it[1].flatten() ]}
kkonganti@0 214 .set { ch_mqc_custom_tbl }
kkonganti@0 215
kkonganti@47 216 TABLE_SUMMARY ( ch_mqc_custom_tbl )
kkonganti@0 217
kkonganti@0 218 DUMP_SOFTWARE_VERSIONS (
kkonganti@0 219 software_versions
kkonganti@0 220 .mix (
kkonganti@0 221 FASTQC.out.versions,
kkonganti@0 222 CENTRIFUGE_CLASSIFY.out.versions,
kkonganti@0 223 CENTRIFUGE_PROCESS.out.versions,
kkonganti@0 224 SEQKIT_GREP.out.versions,
kkonganti@0 225 FLYE_ASSEMBLE.out.versions.ifEmpty(null),
kkonganti@0 226 KRAKEN2_CLASSIFY.out.versions.ifEmpty(null),
kkonganti@0 227 KRAKEN2_EXTRACT_CONTIGS.out.versions.ifEmpty(null),
kkonganti@0 228 SEROTYPEFINDER.out.versions.ifEmpty(null),
kkonganti@0 229 SEQSERO2.out.versions.ifEmpty(null),
kkonganti@0 230 MLST.out.versions.ifEmpty(null),
kkonganti@0 231 ABRICATE_RUN.out.versions.ifEmpty(null),
kkonganti@0 232 ABRICATE_SUMMARY.out.versions.ifEmpty(null),
kkonganti@0 233 TABLE_SUMMARY.out.versions.ifEmpty(null)
kkonganti@0 234 )
kkonganti@0 235 .unique()
kkonganti@0 236 .collectFile(name: 'collected_versions.yml')
kkonganti@0 237 )
kkonganti@0 238
kkonganti@0 239 DUMP_SOFTWARE_VERSIONS
kkonganti@0 240 .out
kkonganti@0 241 .mqc_yml
kkonganti@0 242 .concat (
kkonganti@0 243 ch_mqc_classify,
kkonganti@0 244 TABLE_SUMMARY.out.mqc_yml
kkonganti@0 245 )
kkonganti@0 246 .collect()
kkonganti@0 247 .set { ch_multiqc }
kkonganti@0 248
kkonganti@47 249 MULTIQC ( ch_multiqc )
kkonganti@0 250 }
kkonganti@0 251
kkonganti@0 252 /*
kkonganti@0 253 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0 254 ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG
kkonganti@0 255 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0 256 */
kkonganti@0 257
kkonganti@0 258 workflow.onComplete {
kkonganti@0 259 if (workflow.success) {
kkonganti@0 260 // CREATE APPROPRIATE DIRECTORIES AND MOVE AS REQUESTED BY STAKEHOLDER(S)
kkonganti@0 261 //
kkonganti@0 262 // Nextflow's .moveTo will error out if directories contain files and it
kkonganti@0 263 // would be complex to include logic to skip directories
kkonganti@0 264 //
kkonganti@0 265 def final_intermediate_dir = "${params.output}${params.fs}${params.pipeline}-steps"
kkonganti@0 266 def final_results_dir = "${params.output}${params.fs}${params.pipeline}-results"
kkonganti@0 267 def kraken2_ext_contigs = file( "${final_intermediate_dir}${params.fs}kraken2_extract_contigs", type: 'dir' )
kkonganti@0 268 def final_intermediate = file( final_intermediate_dir, type: 'dir' )
kkonganti@0 269 def final_results = file( final_results_dir, type: 'dir' )
kkonganti@0 270 def pipeline_output = file( params.output, type: 'dir' )
kkonganti@0 271
kkonganti@0 272 if ( !final_intermediate.exists() ) {
kkonganti@0 273 final_intermediate.mkdirs()
kkonganti@0 274
kkonganti@0 275 FileHelper.visitFiles(Paths.get("${params.output}"), '*') {
kkonganti@0 276 if ( !(it.name ==~ /^(${params.cfsanpipename}|multiqc|\.nextflow|${workflow.workDir.name}|${params.pipeline}).*/) ) {
kkonganti@0 277 FileHelper.movePath(
kkonganti@0 278 it, Paths.get( "${final_intermediate_dir}${params.fs}${it.name}" )
kkonganti@0 279 )
kkonganti@0 280 }
kkonganti@0 281 }
kkonganti@0 282 }
kkonganti@0 283
kkonganti@0 284 if ( kraken2_ext_contigs.exists() && !final_results.exists() ) {
kkonganti@0 285 final_results.mkdirs()
kkonganti@0 286
kkonganti@0 287 FileHelper.movePath(
kkonganti@0 288 Paths.get( "${final_intermediate_dir}${params.fs}kraken2_extract_contigs" ),
kkonganti@0 289 Paths.get( "${final_results_dir}${params.fs}kraken2_extract_contigs" )
kkonganti@0 290 )
kkonganti@0 291 }
kkonganti@0 292
kkonganti@0 293 sendMail()
kkonganti@0 294 }
kkonganti@0 295 }
kkonganti@0 296
kkonganti@0 297 workflow.onError {
kkonganti@0 298 sendMail()
kkonganti@0 299 }
kkonganti@0 300
kkonganti@0 301 /*
kkonganti@0 302 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0 303 HELPER METHODS FOR CENTRIFLAKEN WORKFLOW
kkonganti@0 304 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0 305 */
kkonganti@0 306
kkonganti@0 307 def help() {
kkonganti@0 308
kkonganti@0 309 Map helptext = [:]
kkonganti@0 310
kkonganti@47 311 helptext.putAll (
kkonganti@0 312 fastqEntryPointHelp() +
kkonganti@0 313 kraken2Help(params).text +
kkonganti@0 314 centrifugeHelp(params).text +
kkonganti@0 315 flyeHelp(params).text +
kkonganti@0 316 serotypefinderHelp(params).text +
kkonganti@0 317 seqsero2Help(params).text +
kkonganti@0 318 mlstHelp(params).text +
kkonganti@0 319 abricateHelp(params).text +
kkonganti@0 320 wrapUpHelp()
kkonganti@0 321 )
kkonganti@0 322
kkonganti@0 323 return addPadding(helptext)
kkonganti@0 324 }