Mercurial > repos > kkonganti > cfsan_centriflaken

annotate 0.3.0/workflows/centriflaken.nf @ 93:3f367a0de778

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"planemo upload"
author kkonganti
date Tue, 19 Jul 2022 10:14:15 -0400
parents 295c2597a475
children
rev   line source
kkonganti@92 1 // Define any required imports for this specific workflow
kkonganti@92 2 import java.nio.file.Paths
kkonganti@92 3 import nextflow.file.FileHelper
kkonganti@92 4
kkonganti@92 5 // Include any necessary methods
kkonganti@92 6 include { \
kkonganti@92 7 summaryOfParams; stopNow; fastqEntryPointHelp; sendMail; \
kkonganti@92 8 addPadding; wrapUpHelp } from "${params.routines}"
kkonganti@92 9 include { kraken2Help } from "${params.toolshelp}${params.fs}kraken2"
kkonganti@92 10 include { centrifugeHelp } from "${params.toolshelp}${params.fs}centrifuge"
kkonganti@92 11 include { flyeHelp } from "${params.toolshelp}${params.fs}flye"
kkonganti@92 12 include { serotypefinderHelp } from "${params.toolshelp}${params.fs}serotypefinder"
kkonganti@92 13 include { seqsero2Help } from "${params.toolshelp}${params.fs}seqsero2"
kkonganti@92 14 include { mlstHelp } from "${params.toolshelp}${params.fs}mlst"
kkonganti@92 15 include { abricateHelp } from "${params.toolshelp}${params.fs}abricate"
kkonganti@92 16
kkonganti@92 17 // Exit if help requested before any subworkflows
kkonganti@92 18 if (params.help) {
kkonganti@92 19 log.info help()
kkonganti@92 20 exit 0
kkonganti@92 21 }
kkonganti@92 22
kkonganti@92 23 // Include any necessary modules and subworkflows
kkonganti@92 24 include { PROCESS_FASTQ } from "${params.subworkflows}${params.fs}process_fastq"
kkonganti@92 25 include { FASTQC } from "${params.modules}${params.fs}fastqc${params.fs}main"
kkonganti@92 26 include { CENTRIFUGE_CLASSIFY } from "${params.modules}${params.fs}centrifuge${params.fs}classify${params.fs}main"
kkonganti@92 27 include { CENTRIFUGE_PROCESS } from "${params.modules}${params.fs}centrifuge${params.fs}process${params.fs}main"
kkonganti@92 28 include { SEQKIT_GREP } from "${params.modules}${params.fs}seqkit${params.fs}grep${params.fs}main"
kkonganti@92 29 include { FLYE_ASSEMBLE } from "${params.modules}${params.fs}flye${params.fs}assemble${params.fs}main"
kkonganti@92 30 include { KRAKEN2_CLASSIFY } from "${params.modules}${params.fs}kraken2${params.fs}classify${params.fs}main"
kkonganti@92 31 include { KRAKEN2_EXTRACT_CONTIGS } from "${params.modules}${params.fs}kraken2${params.fs}extract_contigs${params.fs}main"
kkonganti@92 32 include { SEROTYPEFINDER } from "${params.modules}${params.fs}serotypefinder${params.fs}main"
kkonganti@92 33 include { SEQSERO2 } from "${params.modules}${params.fs}seqsero2${params.fs}main"
kkonganti@92 34 include { MLST } from "${params.modules}${params.fs}mlst${params.fs}main"
kkonganti@92 35 include { ABRICATE_RUN } from "${params.modules}${params.fs}abricate${params.fs}run${params.fs}main"
kkonganti@92 36 include { ABRICATE_SUMMARY } from "${params.modules}${params.fs}abricate${params.fs}summary${params.fs}main"
kkonganti@92 37 include { TABLE_SUMMARY } from "${params.modules}${params.fs}cat${params.fs}tables${params.fs}main"
kkonganti@92 38 include { MULTIQC } from "${params.modules}${params.fs}multiqc${params.fs}main"
kkonganti@92 39 include { DUMP_SOFTWARE_VERSIONS } from "${params.modules}${params.fs}custom${params.fs}dump_software_versions${params.fs}main"
kkonganti@92 40
kkonganti@92 41
kkonganti@92 42
kkonganti@92 43 /*
kkonganti@92 44 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@92 45 INPUTS AND ANY CHECKS FOR THE CENTRIFLAKEN WORKFLOW
kkonganti@92 46 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@92 47 */
kkonganti@92 48
kkonganti@92 49 def kraken2_db_dir = file ( "${params.kraken2_db}" )
kkonganti@92 50 def centrifuge_x = file ( "${params.centrifuge_x}" )
kkonganti@92 51 def reads_platform = 0
kkonganti@92 52 def abricate_dbs = [ 'ncbiamrplus', 'resfinder', 'megares', 'argannot' ]
kkonganti@92 53
kkonganti@92 54 reads_platform += (params.flye_nano_raw ? 1 : 0)
kkonganti@92 55 reads_platform += (params.flye_nano_corr ? 1 : 0)
kkonganti@92 56 reads_platform += (params.flye_nano_hq ? 1 : 0)
kkonganti@92 57 reads_platform += (params.flye_pacbio_raw ? 1 : 0)
kkonganti@92 58 reads_platform += (params.flye_pacbio_corr ? 1 : 0)
kkonganti@92 59 reads_platform += (params.flye_pacbio_hifi ? 1 : 0)
kkonganti@92 60
kkonganti@92 61 if (!kraken2_db_dir.exists() || !centrifuge_x.getParent().exists()) {
kkonganti@92 62 stopNow("Please check if the following absolute paths are valid:\n" +
kkonganti@92 63 "${params.kraken2_db}\n${params.centrifuge_x}\n" +
kkonganti@92 64 "Cannot proceed further!")
kkonganti@92 65 }
kkonganti@92 66
kkonganti@92 67 if (reads_platform > 1 || reads_platform == 0) {
kkonganti@92 68 msg_0 = (reads_platform > 1 ? "only" : "at least")
kkonganti@92 69 stopNow("Please mention ${msg_0} one read platform for use with the flye assembler\n" +
kkonganti@92 70 "using any one of the following options:\n" +
kkonganti@92 71 "--flye_nano_raw\n--flye_nano_corr\n--flye_nano_hq\n" +
kkonganti@92 72 "--flye_pacbio_raw\n--flye_pacbio_corr\n--flye_pacbio_hifi")
kkonganti@92 73 }
kkonganti@92 74
kkonganti@92 75 if (params.centrifuge_extract_bug != params.kraken2_extract_bug) {
kkonganti@92 76 stopNow("Please make sure that the bug to be extracted is same\n" +
kkonganti@92 77 "for both --centrifuge_extract_bug and --kraken2_extract_bug options.")
kkonganti@92 78 }
kkonganti@92 79
kkonganti@92 80 /*
kkonganti@92 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@92 82 RUN THE CENTRIFLAKEN WORKFLOW
kkonganti@92 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@92 84 */
kkonganti@92 85
kkonganti@92 86 workflow CENTRIFLAKEN {
kkonganti@92 87 main:
kkonganti@92 88 ch_asm_filtered_contigs = Channel.empty()
kkonganti@92 89 ch_mqc_custom_tbl = Channel.empty()
kkonganti@92 90
kkonganti@92 91 log.info summaryOfParams()
kkonganti@92 92
kkonganti@92 93 PROCESS_FASTQ()
kkonganti@92 94 .processed_reads
kkonganti@92 95 .map {
kkonganti@92 96 meta, fastq ->
kkonganti@92 97 meta.centrifuge_x = params.centrifuge_x
kkonganti@92 98 meta.kraken2_db = params.kraken2_db
kkonganti@92 99 [meta, fastq]
kkonganti@92 100 }
kkonganti@92 101 .set { ch_processed_reads }
kkonganti@92 102
kkonganti@92 103 PROCESS_FASTQ
kkonganti@92 104 .out
kkonganti@92 105 .versions
kkonganti@92 106 .set { software_versions }
kkonganti@92 107
kkonganti@92 108 FASTQC ( ch_processed_reads )
kkonganti@92 109
kkonganti@92 110 CENTRIFUGE_CLASSIFY ( ch_processed_reads )
kkonganti@92 111
kkonganti@92 112 CENTRIFUGE_PROCESS (
kkonganti@92 113 CENTRIFUGE_CLASSIFY.out.report
kkonganti@92 114 .join( CENTRIFUGE_CLASSIFY.out.output )
kkonganti@92 115 )
kkonganti@92 116
kkonganti@92 117 ch_processed_reads.join ( CENTRIFUGE_PROCESS.out.extracted )
kkonganti@92 118 .set { ch_centrifuge_extracted }
kkonganti@92 119
kkonganti@92 120 SEQKIT_GREP ( ch_centrifuge_extracted )
kkonganti@92 121
kkonganti@92 122 FLYE_ASSEMBLE ( SEQKIT_GREP.out.fastx )
kkonganti@92 123
kkonganti@92 124 FLYE_ASSEMBLE
kkonganti@92 125 .out
kkonganti@92 126 .assembly
kkonganti@92 127 .set { ch_flye_assembly }
kkonganti@92 128
kkonganti@92 129 ch_flye_assembly.ifEmpty { [ false, false ] }
kkonganti@92 130
kkonganti@92 131 KRAKEN2_CLASSIFY ( ch_flye_assembly )
kkonganti@92 132
kkonganti@92 133 KRAKEN2_EXTRACT_CONTIGS (
kkonganti@92 134 ch_flye_assembly
kkonganti@92 135 .join( KRAKEN2_CLASSIFY.out.kraken_output ),
kkonganti@92 136 params.kraken2_extract_bug
kkonganti@92 137 )
kkonganti@92 138
kkonganti@92 139 KRAKEN2_EXTRACT_CONTIGS
kkonganti@92 140 .out
kkonganti@92 141 .asm_filtered_contigs
kkonganti@92 142 .map {
kkonganti@92 143 meta, fastq ->
kkonganti@92 144 meta.organism = params.kraken2_extract_bug.split(/\s+/)[0].capitalize()
kkonganti@92 145 meta.serotypefinder_db = params.serotypefinder_db
kkonganti@92 146 [meta, fastq]
kkonganti@92 147 }
kkonganti@92 148 .set { ch_asm_filtered_contigs }
kkonganti@92 149
kkonganti@92 150 SEROTYPEFINDER ( ch_asm_filtered_contigs )
kkonganti@92 151
kkonganti@92 152 SEQSERO2 ( ch_asm_filtered_contigs )
kkonganti@92 153
kkonganti@92 154 MLST ( ch_asm_filtered_contigs )
kkonganti@92 155
kkonganti@92 156 ABRICATE_RUN (
kkonganti@92 157 ch_asm_filtered_contigs,
kkonganti@92 158 abricate_dbs
kkonganti@92 159 )
kkonganti@92 160
kkonganti@92 161 ABRICATE_RUN
kkonganti@92 162 .out
kkonganti@92 163 .abricated
kkonganti@92 164 .map { meta, abres -> [ abricate_dbs, abres ] }
kkonganti@92 165 .groupTuple(by: [0])
kkonganti@92 166 .map { it -> tuple ( it[0], it[1].flatten() ) }
kkonganti@92 167 .set { ch_abricated }
kkonganti@92 168
kkonganti@92 169 ABRICATE_SUMMARY ( ch_abricated )
kkonganti@92 170
kkonganti@92 171 // ABRICATE_SUMMARY.out.ecoli_vf.set { ch_abricate_summary_ecoli_vf }
kkonganti@92 172 // ch_abricate_summary_ecoli_vf.ifEmpty { [ false, false ] }
kkonganti@92 173
kkonganti@92 174 CENTRIFUGE_CLASSIFY.out.kreport
kkonganti@92 175 .map { meta, kreport -> [ kreport ] }
kkonganti@92 176 .flatten()
kkonganti@92 177 .concat (
kkonganti@92 178 KRAKEN2_CLASSIFY.out.kraken_report
kkonganti@92 179 .map { meta, kreport -> [ kreport ] }
kkonganti@92 180 .flatten(),
kkonganti@92 181 FASTQC.out.zip
kkonganti@92 182 .map { meta, zip -> [ zip ] }
kkonganti@92 183 .flatten()
kkonganti@92 184 )
kkonganti@92 185 .set { ch_mqc_classify }
kkonganti@92 186
kkonganti@92 187 if (params.serotypefinder_run) {
kkonganti@92 188 SEROTYPEFINDER
kkonganti@92 189 .out
kkonganti@92 190 .serotyped
kkonganti@92 191 .map { meta, tsv -> [ 'serotypefinder', tsv ] }
kkonganti@92 192 .groupTuple(by: [0])
kkonganti@92 193 .map { it -> tuple ( it[0], it[1].flatten() ) }
kkonganti@92 194 .set { ch_mqc_custom_tbl }
kkonganti@92 195 } else if (params.seqsero2_run) {
kkonganti@92 196 SEQSERO2
kkonganti@92 197 .out
kkonganti@92 198 .serotyped
kkonganti@92 199 .map { meta, tsv -> [ 'seqsero2', tsv ] }
kkonganti@92 200 .groupTuple(by: [0])
kkonganti@92 201 .map { it -> tuple ( it[0], it[1].flatten() ) }
kkonganti@92 202 .set { ch_mqc_custom_tbl }
kkonganti@92 203 }
kkonganti@92 204
kkonganti@92 205 ch_mqc_custom_tbl
kkonganti@92 206 .concat (
kkonganti@92 207 ABRICATE_SUMMARY.out.ncbiamrplus.map{ it -> tuple ( it[0], it[1] )},
kkonganti@92 208 ABRICATE_SUMMARY.out.resfinder.map{ it -> tuple ( it[0], it[1] )},
kkonganti@92 209 ABRICATE_SUMMARY.out.megares.map{ it -> tuple ( it[0], it[1] )},
kkonganti@92 210 ABRICATE_SUMMARY.out.argannot.map{ it -> tuple ( it[0], it[1] )},
kkonganti@92 211 )
kkonganti@92 212 .groupTuple(by: [0])
kkonganti@92 213 .map { it -> [ it[0], it[1].flatten() ]}
kkonganti@92 214 .set { ch_mqc_custom_tbl }
kkonganti@92 215
kkonganti@92 216 TABLE_SUMMARY ( ch_mqc_custom_tbl )
kkonganti@92 217
kkonganti@92 218 DUMP_SOFTWARE_VERSIONS (
kkonganti@92 219 software_versions
kkonganti@92 220 .mix (
kkonganti@92 221 FASTQC.out.versions,
kkonganti@92 222 CENTRIFUGE_CLASSIFY.out.versions,
kkonganti@92 223 CENTRIFUGE_PROCESS.out.versions,
kkonganti@92 224 SEQKIT_GREP.out.versions,
kkonganti@92 225 FLYE_ASSEMBLE.out.versions.ifEmpty(null),
kkonganti@92 226 KRAKEN2_CLASSIFY.out.versions.ifEmpty(null),
kkonganti@92 227 KRAKEN2_EXTRACT_CONTIGS.out.versions.ifEmpty(null),
kkonganti@92 228 SEROTYPEFINDER.out.versions.ifEmpty(null),
kkonganti@92 229 SEQSERO2.out.versions.ifEmpty(null),
kkonganti@92 230 MLST.out.versions.ifEmpty(null),
kkonganti@92 231 ABRICATE_RUN.out.versions.ifEmpty(null),
kkonganti@92 232 ABRICATE_SUMMARY.out.versions.ifEmpty(null),
kkonganti@92 233 TABLE_SUMMARY.out.versions.ifEmpty(null)
kkonganti@92 234 )
kkonganti@92 235 .unique()
kkonganti@92 236 .collectFile(name: 'collected_versions.yml')
kkonganti@92 237 )
kkonganti@92 238
kkonganti@92 239 DUMP_SOFTWARE_VERSIONS
kkonganti@92 240 .out
kkonganti@92 241 .mqc_yml
kkonganti@92 242 .concat (
kkonganti@92 243 ch_mqc_classify,
kkonganti@92 244 TABLE_SUMMARY.out.mqc_yml
kkonganti@92 245 )
kkonganti@92 246 .collect()
kkonganti@92 247 .set { ch_multiqc }
kkonganti@92 248
kkonganti@92 249 MULTIQC ( ch_multiqc )
kkonganti@92 250 }
kkonganti@92 251
kkonganti@92 252 /*
kkonganti@92 253 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@92 254 ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG
kkonganti@92 255 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@92 256 */
kkonganti@92 257
kkonganti@92 258 workflow.onComplete {
kkonganti@92 259 if (workflow.success) {
kkonganti@92 260 // CREATE APPROPRIATE DIRECTORIES AND MOVE AS REQUESTED BY STAKEHOLDER(S)
kkonganti@92 261 //
kkonganti@92 262 // Nextflow's .moveTo will error out if directories contain files and it
kkonganti@92 263 // would be complex to include logic to skip directories
kkonganti@92 264 //
kkonganti@92 265 def final_intermediate_dir = "${params.output}${params.fs}${params.pipeline}-steps"
kkonganti@92 266 def final_results_dir = "${params.output}${params.fs}${params.pipeline}-results"
kkonganti@92 267 def kraken2_ext_contigs = file( "${final_intermediate_dir}${params.fs}kraken2_extract_contigs", type: 'dir' )
kkonganti@92 268 def final_intermediate = file( final_intermediate_dir, type: 'dir' )
kkonganti@92 269 def final_results = file( final_results_dir, type: 'dir' )
kkonganti@92 270 def pipeline_output = file( params.output, type: 'dir' )
kkonganti@92 271
kkonganti@92 272 if ( !final_intermediate.exists() ) {
kkonganti@92 273 final_intermediate.mkdirs()
kkonganti@92 274
kkonganti@92 275 FileHelper.visitFiles(Paths.get("${params.output}"), '*') {
kkonganti@92 276 if ( !(it.name ==~ /^(${params.cfsanpipename}|multiqc|\.nextflow|${workflow.workDir.name}|${params.pipeline}).*/) ) {
kkonganti@92 277 FileHelper.movePath(
kkonganti@92 278 it, Paths.get( "${final_intermediate_dir}${params.fs}${it.name}" )
kkonganti@92 279 )
kkonganti@92 280 }
kkonganti@92 281 }
kkonganti@92 282 }
kkonganti@92 283
kkonganti@92 284 if ( kraken2_ext_contigs.exists() && !final_results.exists() ) {
kkonganti@92 285 final_results.mkdirs()
kkonganti@92 286
kkonganti@92 287 FileHelper.movePath(
kkonganti@92 288 Paths.get( "${final_intermediate_dir}${params.fs}kraken2_extract_contigs" ),
kkonganti@92 289 Paths.get( "${final_results_dir}${params.fs}kraken2_extract_contigs" )
kkonganti@92 290 )
kkonganti@92 291 }
kkonganti@92 292
kkonganti@92 293 sendMail()
kkonganti@92 294 }
kkonganti@92 295 }
kkonganti@92 296
kkonganti@92 297 workflow.onError {
kkonganti@92 298 sendMail()
kkonganti@92 299 }
kkonganti@92 300
kkonganti@92 301 /*
kkonganti@92 302 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@92 303 HELPER METHODS FOR CENTRIFLAKEN WORKFLOW
kkonganti@92 304 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@92 305 */
kkonganti@92 306
kkonganti@92 307 def help() {
kkonganti@92 308
kkonganti@92 309 Map helptext = [:]
kkonganti@92 310
kkonganti@92 311 helptext.putAll (
kkonganti@92 312 fastqEntryPointHelp() +
kkonganti@92 313 kraken2Help(params).text +
kkonganti@92 314 centrifugeHelp(params).text +
kkonganti@92 315 flyeHelp(params).text +
kkonganti@92 316 serotypefinderHelp(params).text +
kkonganti@92 317 seqsero2Help(params).text +
kkonganti@92 318 mlstHelp(params).text +
kkonganti@92 319 abricateHelp(params).text +
kkonganti@92 320 wrapUpHelp()
kkonganti@92 321 )
kkonganti@92 322
kkonganti@92 323 return addPadding(helptext)
kkonganti@92 324 }