Mercurial > repos > kkonganti > cfsan_centriflaken

annotate 0.4.0/workflows/centriflaken.nf @ 101:ce6d9548fe89

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"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
parents
children 17890124001d
rev   line source
kkonganti@101 1 // Define any required imports for this specific workflow
kkonganti@101 2 import java.nio.file.Paths
kkonganti@101 3 import nextflow.file.FileHelper
kkonganti@101 4
kkonganti@101 5 // Include any necessary methods
kkonganti@101 6 include { \
kkonganti@101 7 summaryOfParams; stopNow; fastqEntryPointHelp; sendMail; \
kkonganti@101 8 addPadding; wrapUpHelp } from "${params.routines}"
kkonganti@101 9 include { kraken2Help } from "${params.toolshelp}${params.fs}kraken2"
kkonganti@101 10 include { centrifugeHelp } from "${params.toolshelp}${params.fs}centrifuge"
kkonganti@101 11 include { flyeHelp } from "${params.toolshelp}${params.fs}flye"
kkonganti@101 12 include { serotypefinderHelp } from "${params.toolshelp}${params.fs}serotypefinder"
kkonganti@101 13 include { seqsero2Help } from "${params.toolshelp}${params.fs}seqsero2"
kkonganti@101 14 include { mlstHelp } from "${params.toolshelp}${params.fs}mlst"
kkonganti@101 15 include { abricateHelp } from "${params.toolshelp}${params.fs}abricate"
kkonganti@101 16
kkonganti@101 17 // Exit if help requested before any subworkflows
kkonganti@101 18 if (params.help) {
kkonganti@101 19 log.info help()
kkonganti@101 20 exit 0
kkonganti@101 21 }
kkonganti@101 22
kkonganti@101 23 // Include any necessary modules and subworkflows
kkonganti@101 24 include { PROCESS_FASTQ } from "${params.subworkflows}${params.fs}process_fastq"
kkonganti@101 25 include { FASTQC } from "${params.modules}${params.fs}fastqc${params.fs}main"
kkonganti@101 26 include { CENTRIFUGE_CLASSIFY } from "${params.modules}${params.fs}centrifuge${params.fs}classify${params.fs}main"
kkonganti@101 27 include { CENTRIFUGE_PROCESS } from "${params.modules}${params.fs}centrifuge${params.fs}process${params.fs}main"
kkonganti@101 28 include { SEQKIT_GREP } from "${params.modules}${params.fs}seqkit${params.fs}grep${params.fs}main"
kkonganti@101 29 include { FLYE_ASSEMBLE } from "${params.modules}${params.fs}flye${params.fs}assemble${params.fs}main"
kkonganti@101 30 include { KRAKEN2_CLASSIFY } from "${params.modules}${params.fs}kraken2${params.fs}classify${params.fs}main"
kkonganti@101 31 include { KRAKEN2_EXTRACT_CONTIGS } from "${params.modules}${params.fs}kraken2${params.fs}extract_contigs${params.fs}main"
kkonganti@101 32 include { SEROTYPEFINDER } from "${params.modules}${params.fs}serotypefinder${params.fs}main"
kkonganti@101 33 include { SEQSERO2 } from "${params.modules}${params.fs}seqsero2${params.fs}main"
kkonganti@101 34 include { MLST } from "${params.modules}${params.fs}mlst${params.fs}main"
kkonganti@101 35 include { ABRICATE_RUN } from "${params.modules}${params.fs}abricate${params.fs}run${params.fs}main"
kkonganti@101 36 include { ABRICATE_SUMMARY } from "${params.modules}${params.fs}abricate${params.fs}summary${params.fs}main"
kkonganti@101 37 include { TABLE_SUMMARY } from "${params.modules}${params.fs}cat${params.fs}tables${params.fs}main"
kkonganti@101 38 include { MULTIQC } from "${params.modules}${params.fs}multiqc${params.fs}main"
kkonganti@101 39 include { DUMP_SOFTWARE_VERSIONS } from "${params.modules}${params.fs}custom${params.fs}dump_software_versions${params.fs}main"
kkonganti@101 40
kkonganti@101 41
kkonganti@101 42
kkonganti@101 43 /*
kkonganti@101 44 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@101 45 INPUTS AND ANY CHECKS FOR THE CENTRIFLAKEN WORKFLOW
kkonganti@101 46 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@101 47 */
kkonganti@101 48
kkonganti@101 49 def kraken2_db_dir = file ( "${params.kraken2_db}" )
kkonganti@101 50 def centrifuge_x = file ( "${params.centrifuge_x}" )
kkonganti@101 51 def reads_platform = 0
kkonganti@101 52 def abricate_dbs = [ 'ncbiamrplus', 'resfinder', 'megares', 'argannot' ]
kkonganti@101 53
kkonganti@101 54 reads_platform += (params.flye_nano_raw ? 1 : 0)
kkonganti@101 55 reads_platform += (params.flye_nano_corr ? 1 : 0)
kkonganti@101 56 reads_platform += (params.flye_nano_hq ? 1 : 0)
kkonganti@101 57 reads_platform += (params.flye_pacbio_raw ? 1 : 0)
kkonganti@101 58 reads_platform += (params.flye_pacbio_corr ? 1 : 0)
kkonganti@101 59 reads_platform += (params.flye_pacbio_hifi ? 1 : 0)
kkonganti@101 60
kkonganti@101 61 if (!kraken2_db_dir.exists() || !centrifuge_x.getParent().exists()) {
kkonganti@101 62 stopNow("Please check if the following absolute paths are valid:\n" +
kkonganti@101 63 "${params.kraken2_db}\n${params.centrifuge_x}\n" +
kkonganti@101 64 "Cannot proceed further!")
kkonganti@101 65 }
kkonganti@101 66
kkonganti@101 67 if (reads_platform > 1 || reads_platform == 0) {
kkonganti@101 68 msg_0 = (reads_platform > 1 ? "only" : "at least")
kkonganti@101 69 stopNow("Please mention ${msg_0} one read platform for use with the flye assembler\n" +
kkonganti@101 70 "using any one of the following options:\n" +
kkonganti@101 71 "--flye_nano_raw\n--flye_nano_corr\n--flye_nano_hq\n" +
kkonganti@101 72 "--flye_pacbio_raw\n--flye_pacbio_corr\n--flye_pacbio_hifi")
kkonganti@101 73 }
kkonganti@101 74
kkonganti@101 75 if (params.centrifuge_extract_bug != params.kraken2_extract_bug) {
kkonganti@101 76 stopNow("Please make sure that the bug to be extracted is same\n" +
kkonganti@101 77 "for both --centrifuge_extract_bug and --kraken2_extract_bug options.")
kkonganti@101 78 }
kkonganti@101 79
kkonganti@101 80 /*
kkonganti@101 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@101 82 RUN THE CENTRIFLAKEN WORKFLOW
kkonganti@101 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@101 84 */
kkonganti@101 85
kkonganti@101 86 workflow CENTRIFLAKEN {
kkonganti@101 87 main:
kkonganti@101 88 ch_asm_filtered_contigs = Channel.empty()
kkonganti@101 89 ch_mqc_custom_tbl = Channel.empty()
kkonganti@101 90
kkonganti@101 91 log.info summaryOfParams()
kkonganti@101 92
kkonganti@101 93 PROCESS_FASTQ()
kkonganti@101 94 .processed_reads
kkonganti@101 95 .map {
kkonganti@101 96 meta, fastq ->
kkonganti@101 97 meta.centrifuge_x = params.centrifuge_x
kkonganti@101 98 meta.kraken2_db = params.kraken2_db
kkonganti@101 99 [meta, fastq]
kkonganti@101 100 }
kkonganti@101 101 .set { ch_processed_reads }
kkonganti@101 102
kkonganti@101 103 PROCESS_FASTQ
kkonganti@101 104 .out
kkonganti@101 105 .versions
kkonganti@101 106 .set { software_versions }
kkonganti@101 107
kkonganti@101 108 FASTQC ( ch_processed_reads )
kkonganti@101 109
kkonganti@101 110 CENTRIFUGE_CLASSIFY ( ch_processed_reads )
kkonganti@101 111
kkonganti@101 112 CENTRIFUGE_PROCESS (
kkonganti@101 113 CENTRIFUGE_CLASSIFY.out.report
kkonganti@101 114 .join( CENTRIFUGE_CLASSIFY.out.output )
kkonganti@101 115 )
kkonganti@101 116
kkonganti@101 117 ch_processed_reads.join ( CENTRIFUGE_PROCESS.out.extracted )
kkonganti@101 118 .set { ch_centrifuge_extracted }
kkonganti@101 119
kkonganti@101 120 SEQKIT_GREP ( ch_centrifuge_extracted )
kkonganti@101 121
kkonganti@101 122 FLYE_ASSEMBLE ( SEQKIT_GREP.out.fastx )
kkonganti@101 123
kkonganti@101 124 FLYE_ASSEMBLE
kkonganti@101 125 .out
kkonganti@101 126 .assembly
kkonganti@101 127 .set { ch_flye_assembly }
kkonganti@101 128
kkonganti@101 129 ch_flye_assembly.ifEmpty { [ false, false ] }
kkonganti@101 130
kkonganti@101 131 KRAKEN2_CLASSIFY ( ch_flye_assembly )
kkonganti@101 132
kkonganti@101 133 KRAKEN2_EXTRACT_CONTIGS (
kkonganti@101 134 ch_flye_assembly
kkonganti@101 135 .join( KRAKEN2_CLASSIFY.out.kraken_output ),
kkonganti@101 136 params.kraken2_extract_bug
kkonganti@101 137 )
kkonganti@101 138
kkonganti@101 139 KRAKEN2_EXTRACT_CONTIGS
kkonganti@101 140 .out
kkonganti@101 141 .asm_filtered_contigs
kkonganti@101 142 .map {
kkonganti@101 143 meta, fastq ->
kkonganti@101 144 meta.organism = params.kraken2_extract_bug.split(/\s+/)[0].capitalize()
kkonganti@101 145 meta.serotypefinder_db = params.serotypefinder_db
kkonganti@101 146 [meta, fastq]
kkonganti@101 147 }
kkonganti@101 148 .set { ch_asm_filtered_contigs }
kkonganti@101 149
kkonganti@101 150 SEROTYPEFINDER ( ch_asm_filtered_contigs )
kkonganti@101 151
kkonganti@101 152 SEQSERO2 ( ch_asm_filtered_contigs )
kkonganti@101 153
kkonganti@101 154 MLST ( ch_asm_filtered_contigs )
kkonganti@101 155
kkonganti@101 156 ABRICATE_RUN (
kkonganti@101 157 ch_asm_filtered_contigs,
kkonganti@101 158 abricate_dbs
kkonganti@101 159 )
kkonganti@101 160
kkonganti@101 161 ABRICATE_RUN
kkonganti@101 162 .out
kkonganti@101 163 .abricated
kkonganti@101 164 .map { meta, abres -> [ abricate_dbs, abres ] }
kkonganti@101 165 .groupTuple(by: [0])
kkonganti@101 166 .map { it -> tuple ( it[0], it[1].flatten() ) }
kkonganti@101 167 .set { ch_abricated }
kkonganti@101 168
kkonganti@101 169 ABRICATE_SUMMARY ( ch_abricated )
kkonganti@101 170
kkonganti@101 171 // ABRICATE_SUMMARY.out.ecoli_vf.set { ch_abricate_summary_ecoli_vf }
kkonganti@101 172 // ch_abricate_summary_ecoli_vf.ifEmpty { [ false, false ] }
kkonganti@101 173
kkonganti@101 174 CENTRIFUGE_CLASSIFY.out.kreport
kkonganti@101 175 .map { meta, kreport -> [ kreport ] }
kkonganti@101 176 .flatten()
kkonganti@101 177 .concat (
kkonganti@101 178 KRAKEN2_CLASSIFY.out.kraken_report
kkonganti@101 179 .map { meta, kreport -> [ kreport ] }
kkonganti@101 180 .flatten(),
kkonganti@101 181 FASTQC.out.zip
kkonganti@101 182 .map { meta, zip -> [ zip ] }
kkonganti@101 183 .flatten()
kkonganti@101 184 )
kkonganti@101 185 .set { ch_mqc_classify }
kkonganti@101 186
kkonganti@101 187 if (params.serotypefinder_run) {
kkonganti@101 188 SEROTYPEFINDER
kkonganti@101 189 .out
kkonganti@101 190 .serotyped
kkonganti@101 191 .map { meta, tsv -> [ 'serotypefinder', tsv ] }
kkonganti@101 192 .groupTuple(by: [0])
kkonganti@101 193 .map { it -> tuple ( it[0], it[1].flatten() ) }
kkonganti@101 194 .set { ch_mqc_custom_tbl }
kkonganti@101 195 } else if (params.seqsero2_run) {
kkonganti@101 196 SEQSERO2
kkonganti@101 197 .out
kkonganti@101 198 .serotyped
kkonganti@101 199 .map { meta, tsv -> [ 'seqsero2', tsv ] }
kkonganti@101 200 .groupTuple(by: [0])
kkonganti@101 201 .map { it -> tuple ( it[0], it[1].flatten() ) }
kkonganti@101 202 .set { ch_mqc_custom_tbl }
kkonganti@101 203 }
kkonganti@101 204
kkonganti@101 205 ch_mqc_custom_tbl
kkonganti@101 206 .concat (
kkonganti@101 207 ABRICATE_SUMMARY.out.ncbiamrplus.map{ it -> tuple ( it[0], it[1] )},
kkonganti@101 208 ABRICATE_SUMMARY.out.resfinder.map{ it -> tuple ( it[0], it[1] )},
kkonganti@101 209 ABRICATE_SUMMARY.out.megares.map{ it -> tuple ( it[0], it[1] )},
kkonganti@101 210 ABRICATE_SUMMARY.out.argannot.map{ it -> tuple ( it[0], it[1] )},
kkonganti@101 211 )
kkonganti@101 212 .groupTuple(by: [0])
kkonganti@101 213 .map { it -> [ it[0], it[1].flatten() ]}
kkonganti@101 214 .set { ch_mqc_custom_tbl }
kkonganti@101 215
kkonganti@101 216 TABLE_SUMMARY ( ch_mqc_custom_tbl )
kkonganti@101 217
kkonganti@101 218 DUMP_SOFTWARE_VERSIONS (
kkonganti@101 219 software_versions
kkonganti@101 220 .mix (
kkonganti@101 221 FASTQC.out.versions,
kkonganti@101 222 CENTRIFUGE_CLASSIFY.out.versions,
kkonganti@101 223 CENTRIFUGE_PROCESS.out.versions,
kkonganti@101 224 SEQKIT_GREP.out.versions,
kkonganti@101 225 FLYE_ASSEMBLE.out.versions.ifEmpty(null),
kkonganti@101 226 KRAKEN2_CLASSIFY.out.versions.ifEmpty(null),
kkonganti@101 227 KRAKEN2_EXTRACT_CONTIGS.out.versions.ifEmpty(null),
kkonganti@101 228 SEROTYPEFINDER.out.versions.ifEmpty(null),
kkonganti@101 229 SEQSERO2.out.versions.ifEmpty(null),
kkonganti@101 230 MLST.out.versions.ifEmpty(null),
kkonganti@101 231 ABRICATE_RUN.out.versions.ifEmpty(null),
kkonganti@101 232 ABRICATE_SUMMARY.out.versions.ifEmpty(null),
kkonganti@101 233 TABLE_SUMMARY.out.versions.ifEmpty(null)
kkonganti@101 234 )
kkonganti@101 235 .unique()
kkonganti@101 236 .collectFile(name: 'collected_versions.yml')
kkonganti@101 237 )
kkonganti@101 238
kkonganti@101 239 DUMP_SOFTWARE_VERSIONS
kkonganti@101 240 .out
kkonganti@101 241 .mqc_yml
kkonganti@101 242 .concat (
kkonganti@101 243 ch_mqc_classify,
kkonganti@101 244 TABLE_SUMMARY.out.mqc_yml
kkonganti@101 245 )
kkonganti@101 246 .collect()
kkonganti@101 247 .set { ch_multiqc }
kkonganti@101 248
kkonganti@101 249 MULTIQC ( ch_multiqc )
kkonganti@101 250 }
kkonganti@101 251
kkonganti@101 252 /*
kkonganti@101 253 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@101 254 ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG
kkonganti@101 255 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@101 256 */
kkonganti@101 257
kkonganti@101 258 workflow.onComplete {
kkonganti@101 259 if (workflow.success) {
kkonganti@101 260 // CREATE APPROPRIATE DIRECTORIES AND MOVE AS REQUESTED BY STAKEHOLDER(S)
kkonganti@101 261 //
kkonganti@101 262 // Nextflow's .moveTo will error out if directories contain files and it
kkonganti@101 263 // would be complex to include logic to skip directories
kkonganti@101 264 //
kkonganti@101 265 def final_intermediate_dir = "${params.output}${params.fs}${params.pipeline}-steps"
kkonganti@101 266 def final_results_dir = "${params.output}${params.fs}${params.pipeline}-results"
kkonganti@101 267 def kraken2_ext_contigs = file( "${final_intermediate_dir}${params.fs}kraken2_extract_contigs", type: 'dir' )
kkonganti@101 268 def final_intermediate = file( final_intermediate_dir, type: 'dir' )
kkonganti@101 269 def final_results = file( final_results_dir, type: 'dir' )
kkonganti@101 270 def pipeline_output = file( params.output, type: 'dir' )
kkonganti@101 271
kkonganti@101 272 if ( !final_intermediate.exists() ) {
kkonganti@101 273 final_intermediate.mkdirs()
kkonganti@101 274
kkonganti@101 275 FileHelper.visitFiles(Paths.get("${params.output}"), '*') {
kkonganti@101 276 if ( !(it.name ==~ /^(${params.cfsanpipename}|multiqc|\.nextflow|${workflow.workDir.name}|${params.pipeline}).*/) ) {
kkonganti@101 277 FileHelper.movePath(
kkonganti@101 278 it, Paths.get( "${final_intermediate_dir}${params.fs}${it.name}" )
kkonganti@101 279 )
kkonganti@101 280 }
kkonganti@101 281 }
kkonganti@101 282 }
kkonganti@101 283
kkonganti@101 284 if ( kraken2_ext_contigs.exists() && !final_results.exists() ) {
kkonganti@101 285 final_results.mkdirs()
kkonganti@101 286
kkonganti@101 287 FileHelper.movePath(
kkonganti@101 288 Paths.get( "${final_intermediate_dir}${params.fs}kraken2_extract_contigs" ),
kkonganti@101 289 Paths.get( "${final_results_dir}${params.fs}kraken2_extract_contigs" )
kkonganti@101 290 )
kkonganti@101 291 }
kkonganti@101 292
kkonganti@101 293 sendMail()
kkonganti@101 294 }
kkonganti@101 295 }
kkonganti@101 296
kkonganti@101 297 workflow.onError {
kkonganti@101 298 sendMail()
kkonganti@101 299 }
kkonganti@101 300
kkonganti@101 301 /*
kkonganti@101 302 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@101 303 HELPER METHODS FOR CENTRIFLAKEN WORKFLOW
kkonganti@101 304 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@101 305 */
kkonganti@101 306
kkonganti@101 307 def help() {
kkonganti@101 308
kkonganti@101 309 Map helptext = [:]
kkonganti@101 310
kkonganti@101 311 helptext.putAll (
kkonganti@101 312 fastqEntryPointHelp() +
kkonganti@101 313 kraken2Help(params).text +
kkonganti@101 314 centrifugeHelp(params).text +
kkonganti@101 315 flyeHelp(params).text +
kkonganti@101 316 serotypefinderHelp(params).text +
kkonganti@101 317 seqsero2Help(params).text +
kkonganti@101 318 mlstHelp(params).text +
kkonganti@101 319 abricateHelp(params).text +
kkonganti@101 320 wrapUpHelp()
kkonganti@101 321 )
kkonganti@101 322
kkonganti@101 323 return addPadding(helptext)
kkonganti@101 324 }