Mercurial > repos > kkonganti > hfp_nowayout

annotate 0.5.0/workflows/nowayout.nf @ 0:97cd2f532efe

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planemo upload
author kkonganti
date Mon, 31 Mar 2025 14:50:40 -0400
parents
children 3539fbeb4230
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 java.util.zip.GZIPInputStream
kkonganti@0 4 import java.io.FileInputStream
kkonganti@0 5 import nextflow.file.FileHelper
kkonganti@0 6
kkonganti@0 7
kkonganti@0 8 // Include any necessary methods
kkonganti@0 9 include { \
kkonganti@0 10 summaryOfParams; stopNow; fastqEntryPointHelp; sendMail; \
kkonganti@0 11 addPadding; wrapUpHelp } from "${params.routines}"
kkonganti@0 12 include { fastpHelp } from "${params.toolshelp}${params.fs}fastp"
kkonganti@0 13 include { kmaalignHelp } from "${params.toolshelp}${params.fs}kmaalign"
kkonganti@0 14 include { seqkitgrepHelp } from "${params.toolshelp}${params.fs}seqkitgrep"
kkonganti@0 15 include { salmonidxHelp } from "${params.toolshelp}${params.fs}salmonidx"
kkonganti@0 16 include { sourmashsketchHelp } from "${params.toolshelp}${params.fs}sourmashsketch"
kkonganti@0 17 include { sourmashgatherHelp } from "${params.toolshelp}${params.fs}sourmashgather"
kkonganti@0 18 include { sfhpyHelp } from "${params.toolshelp}${params.fs}sfhpy"
kkonganti@0 19 include { gsalkronapyHelp } from "${params.toolshelp}${params.fs}gsalkronapy"
kkonganti@0 20 include { kronaktimporttextHelp } from "${params.toolshelp}${params.fs}kronaktimporttext"
kkonganti@0 21
kkonganti@0 22 // Exit if help requested before any subworkflows
kkonganti@0 23 if (params.help) {
kkonganti@0 24 log.info help()
kkonganti@0 25 exit 0
kkonganti@0 26 }
kkonganti@0 27
kkonganti@0 28
kkonganti@0 29 // Include any necessary modules and subworkflows
kkonganti@0 30 include { PROCESS_FASTQ } from "${params.subworkflows}${params.fs}process_fastq"
kkonganti@0 31 include { FASTP } from "${params.modules}${params.fs}fastp${params.fs}main"
kkonganti@0 32 include { KMA_ALIGN } from "${params.modules}${params.fs}kma${params.fs}align${params.fs}main"
kkonganti@0 33 include { OTF_GENOME } from "${params.modules}${params.fs}otf_genome${params.fs}main"
kkonganti@0 34 include { SEQKIT_GREP } from "${params.modules}${params.fs}seqkit${params.fs}grep${params.fs}main"
kkonganti@0 35 include { SALMON_INDEX } from "${params.modules}${params.fs}salmon${params.fs}index${params.fs}main"
kkonganti@0 36 include { SALMON_QUANT } from "${params.modules}${params.fs}salmon${params.fs}quant${params.fs}main"
kkonganti@0 37 include { SOURMASH_SKETCH } from "${params.modules}${params.fs}sourmash${params.fs}sketch${params.fs}main"
kkonganti@0 38 include { SOURMASH_SKETCH \
kkonganti@0 39 as REDUCE_DB_IDX } from "${params.modules}${params.fs}sourmash${params.fs}sketch${params.fs}main"
kkonganti@0 40 include { SOURMASH_GATHER } from "${params.modules}${params.fs}sourmash${params.fs}gather${params.fs}main"
kkonganti@0 41 include { NOWAYOUT_RESULTS } from "${params.modules}${params.fs}nowayout_results${params.fs}main"
kkonganti@0 42 include { KRONA_KTIMPORTTEXT } from "${params.modules}${params.fs}krona${params.fs}ktimporttext${params.fs}main"
kkonganti@0 43 include { DUMP_SOFTWARE_VERSIONS } from "${params.modules}${params.fs}custom${params.fs}dump_software_versions${params.fs}main"
kkonganti@0 44 include { MULTIQC } from "${params.modules}${params.fs}multiqc${params.fs}main"
kkonganti@0 45
kkonganti@0 46 /*
kkonganti@0 47 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0 48 INPUTS AND ANY CHECKS FOR THE BETTERCALLSAL WORKFLOW
kkonganti@0 49 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0 50 */
kkonganti@0 51
kkonganti@0 52 def reads_platform = 0
kkonganti@0 53 reads_platform += (params.input ? 1 : 0)
kkonganti@0 54
kkonganti@0 55 if (reads_platform < 1 || reads_platform == 0) {
kkonganti@0 56 stopNow("Please mention at least one absolute path to input folder which contains\n" +
kkonganti@0 57 "FASTQ files sequenced using the --input option.\n" +
kkonganti@0 58 "Ex: --input (Illumina or Generic short reads in FASTQ format)")
kkonganti@0 59 }
kkonganti@0 60
kkonganti@0 61 params.fastp_adapter_fasta ? checkMetadataExists(params.fastp_adapter_fasta, 'Adapter sequences FASTA') : null
kkonganti@0 62 checkMetadataExists(params.lineages_csv, 'Lineages CSV')
kkonganti@0 63 checkMetadataExists(params.kmaalign_idx, 'KMA Indices')
kkonganti@0 64 checkMetadataExists(params.ref_fna, 'FASTA reference')
kkonganti@0 65
kkonganti@0 66 ch_sourmash_lin = file( params.lineages_csv )
kkonganti@0 67
kkonganti@0 68
kkonganti@0 69 /*
kkonganti@0 70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0 71 RUN THE BETTERCALLSAL WORKFLOW
kkonganti@0 72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0 73 */
kkonganti@0 74
kkonganti@0 75 workflow NOWAYOUT {
kkonganti@0 76 main:
kkonganti@0 77 log.info summaryOfParams()
kkonganti@0 78
kkonganti@0 79 PROCESS_FASTQ()
kkonganti@0 80
kkonganti@0 81 PROCESS_FASTQ.out.versions
kkonganti@0 82 .set { software_versions }
kkonganti@0 83
kkonganti@0 84 PROCESS_FASTQ.out.processed_reads
kkonganti@0 85 .set { ch_processed_reads }
kkonganti@0 86
kkonganti@0 87 ch_processed_reads
kkonganti@0 88 .map { meta, fastq ->
kkonganti@0 89 meta.get_kma_hit_accs = true
kkonganti@0 90 meta.salmon_decoys = params.dummyfile
kkonganti@0 91 meta.salmon_lib_type = (params.salmonalign_libtype ?: false)
kkonganti@0 92 meta.kma_t_db = params.kmaalign_idx
kkonganti@0 93 [ meta, fastq ]
kkonganti@0 94 }
kkonganti@0 95 .filter { meta, fastq ->
kkonganti@0 96 fq_file = ( fastq.getClass().toString() =~ /ArrayList/ ? fastq : [ fastq ] )
kkonganti@0 97 fq_gzip = new GZIPInputStream( new FileInputStream( fq_file[0].toAbsolutePath().toString() ) )
kkonganti@0 98 fq_gzip.read() != -1
kkonganti@0 99 }
kkonganti@0 100 .set { ch_processed_reads }
kkonganti@0 101
kkonganti@0 102 FASTP( ch_processed_reads )
kkonganti@0 103
kkonganti@0 104 FASTP.out.json
kkonganti@0 105 .map { meta, json ->
kkonganti@0 106 json
kkonganti@0 107 }
kkonganti@0 108 .collect()
kkonganti@0 109 .set { ch_multiqc }
kkonganti@0 110
kkonganti@0 111 KMA_ALIGN(
kkonganti@0 112 FASTP.out.passed_reads
kkonganti@0 113 .map { meta, fastq ->
kkonganti@0 114 [meta, fastq, []]
kkonganti@0 115 }
kkonganti@0 116 )
kkonganti@0 117
kkonganti@0 118 OTF_GENOME(
kkonganti@0 119 KMA_ALIGN.out.hits
kkonganti@0 120 .join(KMA_ALIGN.out.frags)
kkonganti@0 121 )
kkonganti@0 122
kkonganti@0 123 OTF_GENOME.out.reads_extracted
kkonganti@0 124 .filter { meta, fasta ->
kkonganti@0 125 fa_file = ( fasta.getClass().toString() =~ /ArrayList/ ? fasta : [ fasta ] )
kkonganti@0 126 fa_gzip = new GZIPInputStream( new FileInputStream( fa_file[0].toAbsolutePath().toString() ) )
kkonganti@0 127 fa_gzip.read() != -1
kkonganti@0 128 }
kkonganti@0 129 .set { ch_mito_aln_reads }
kkonganti@0 130
kkonganti@0 131 SEQKIT_GREP(
kkonganti@0 132 KMA_ALIGN.out.hits
kkonganti@0 133 .filter { meta, mapped_refs ->
kkonganti@0 134 patterns = file( mapped_refs )
kkonganti@0 135 patterns.size() > 0
kkonganti@0 136 }
kkonganti@0 137 .map { meta, mapped_refs ->
kkonganti@0 138 [meta, params.ref_fna, mapped_refs]
kkonganti@0 139 }
kkonganti@0 140 )
kkonganti@0 141
kkonganti@0 142 SALMON_INDEX( SEQKIT_GREP.out.fastx )
kkonganti@0 143
kkonganti@0 144 SALMON_QUANT(
kkonganti@0 145 ch_mito_aln_reads
kkonganti@0 146 .join( SALMON_INDEX.out.idx )
kkonganti@0 147 )
kkonganti@0 148
kkonganti@0 149 REDUCE_DB_IDX(
kkonganti@0 150 SEQKIT_GREP.out.fastx,
kkonganti@0 151 true,
kkonganti@0 152 false,
kkonganti@0 153 'db'
kkonganti@0 154 )
kkonganti@0 155
kkonganti@0 156 SOURMASH_SKETCH(
kkonganti@0 157 ch_mito_aln_reads,
kkonganti@0 158 false,
kkonganti@0 159 false,
kkonganti@0 160 'query'
kkonganti@0 161 )
kkonganti@0 162
kkonganti@0 163 SOURMASH_GATHER(
kkonganti@0 164 SOURMASH_SKETCH.out.signatures
kkonganti@0 165 .join( REDUCE_DB_IDX.out.signatures ),
kkonganti@0 166 [], [], [], []
kkonganti@0 167 )
kkonganti@0 168
kkonganti@0 169 // SOURMASH_TAX_METAGENOME(
kkonganti@0 170 // SOURMASH_GATHER.out.result
kkonganti@0 171 // .groupTuple(by: [0])
kkonganti@0 172 // .map { meta, csv ->
kkonganti@0 173 // [ meta, csv, ch_sourmash_lin ]
kkonganti@0 174 // }
kkonganti@0 175 // )
kkonganti@0 176
kkonganti@0 177 // SOURMASH_TAX_METAGENOME.out.csv
kkonganti@0 178 // .map { meta, csv ->
kkonganti@0 179 // csv
kkonganti@0 180 // }
kkonganti@0 181 // .set { ch_lin_csv }
kkonganti@0 182
kkonganti@0 183 // SOURMASH_TAX_METAGENOME.out.tsv
kkonganti@0 184 // .tap { ch_lin_krona }
kkonganti@0 185 // .map { meta, tsv ->
kkonganti@0 186 // tsv
kkonganti@0 187 // }
kkonganti@0 188 // .tap { ch_lin_tsv }
kkonganti@0 189
kkonganti@0 190 SOURMASH_GATHER.out.result
kkonganti@0 191 .groupTuple(by: [0])
kkonganti@0 192 .map { meta, csv ->
kkonganti@0 193 [ csv ]
kkonganti@0 194 }
kkonganti@0 195 .concat(
kkonganti@0 196 SALMON_QUANT.out.results
kkonganti@0 197 .map { meta, salmon_res ->
kkonganti@0 198 [ salmon_res ]
kkonganti@0 199 }
kkonganti@0 200 )
kkonganti@0 201 .concat(
kkonganti@0 202 SOURMASH_GATHER.out.failed
kkonganti@0 203 .map { meta, failed ->
kkonganti@0 204 [ failed ]
kkonganti@0 205 }
kkonganti@0 206 )
kkonganti@0 207 .concat( OTF_GENOME.out.failed )
kkonganti@0 208 .collect()
kkonganti@0 209 .flatten()
kkonganti@0 210 .collect()
kkonganti@0 211 .set { ch_gene_abn }
kkonganti@0 212
kkonganti@0 213 NOWAYOUT_RESULTS( ch_gene_abn, ch_sourmash_lin )
kkonganti@0 214
kkonganti@0 215 NOWAYOUT_RESULTS.out.tsv
kkonganti@0 216 .flatten()
kkonganti@0 217 .filter { tsv -> tsv.toString() =~ /.*${params.krona_res_suffix}$/ }
kkonganti@0 218 .map { tsv ->
kkonganti@0 219 meta = [:]
kkonganti@0 220 meta.id = "${params.cfsanpipename}_${params.pipeline}_krona"
kkonganti@0 221 [ meta, tsv ]
kkonganti@0 222 }
kkonganti@0 223 .groupTuple(by: [0])
kkonganti@0 224 .set { ch_lin_krona }
kkonganti@0 225
kkonganti@0 226 // ch_lin_tsv
kkonganti@0 227 // .mix( ch_lin_csv )
kkonganti@0 228 // .collect()
kkonganti@0 229 // .set { ch_lin_summary }
kkonganti@0 230
kkonganti@0 231 // SOURMASH_TAX_METAGENOME.out.txt
kkonganti@0 232 // .map { meta, txt ->
kkonganti@0 233 // txt
kkonganti@0 234 // }
kkonganti@0 235 // .collect()
kkonganti@0 236 // .set { ch_lin_kreport }
kkonganti@0 237
kkonganti@0 238 // NOWAYOUT_RESULTS(
kkonganti@0 239 // ch_lin_summary
kkonganti@0 240 // .concat( SOURMASH_GATHER.out.failed )
kkonganti@0 241 // .concat( OTF_GENOME.out.failed )
kkonganti@0 242 // .collect()
kkonganti@0 243 // )
kkonganti@0 244
kkonganti@0 245 KRONA_KTIMPORTTEXT( ch_lin_krona )
kkonganti@0 246
kkonganti@0 247 DUMP_SOFTWARE_VERSIONS(
kkonganti@0 248 software_versions
kkonganti@0 249 .mix (
kkonganti@0 250 FASTP.out.versions,
kkonganti@0 251 KMA_ALIGN.out.versions,
kkonganti@0 252 SEQKIT_GREP.out.versions,
kkonganti@0 253 REDUCE_DB_IDX.out.versions,
kkonganti@0 254 SOURMASH_SKETCH.out.versions,
kkonganti@0 255 SOURMASH_GATHER.out.versions,
kkonganti@0 256 SALMON_INDEX.out.versions,
kkonganti@0 257 SALMON_QUANT.out.versions,
kkonganti@0 258 NOWAYOUT_RESULTS.out.versions,
kkonganti@0 259 KRONA_KTIMPORTTEXT.out.versions
kkonganti@0 260 )
kkonganti@0 261 .unique()
kkonganti@0 262 .collectFile(name: 'collected_versions.yml')
kkonganti@0 263 )
kkonganti@0 264
kkonganti@0 265 DUMP_SOFTWARE_VERSIONS.out.mqc_yml
kkonganti@0 266 .concat(
kkonganti@0 267 ch_multiqc,
kkonganti@0 268 NOWAYOUT_RESULTS.out.mqc_yml
kkonganti@0 269 )
kkonganti@0 270 .collect()
kkonganti@0 271 .flatten()
kkonganti@0 272 .collect()
kkonganti@0 273 .set { ch_multiqc }
kkonganti@0 274
kkonganti@0 275 MULTIQC( ch_multiqc )
kkonganti@0 276 }
kkonganti@0 277
kkonganti@0 278 /*
kkonganti@0 279 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0 280 ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG
kkonganti@0 281 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0 282 */
kkonganti@0 283
kkonganti@0 284 workflow.onComplete {
kkonganti@0 285 if (workflow.success) {
kkonganti@0 286 sendMail()
kkonganti@0 287 }
kkonganti@0 288 }
kkonganti@0 289
kkonganti@0 290 workflow.onError {
kkonganti@0 291 sendMail()
kkonganti@0 292 }
kkonganti@0 293
kkonganti@0 294 /*
kkonganti@0 295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0 296 METHOD TO CHECK METADATA EXISTENCE
kkonganti@0 297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0 298 */
kkonganti@0 299
kkonganti@0 300 def checkMetadataExists(file_path, msg) {
kkonganti@0 301 file_path_obj = file( file_path )
kkonganti@0 302
kkonganti@0 303 if (msg.toString().find(/(?i)KMA/)) {
kkonganti@0 304 if (!file_path_obj.parent.exists() || file_path_obj.parent.size() == 0) {
kkonganti@0 305 stopNow("Please check if your ${msg}\n" +
kkonganti@0 306 "[ ${file_path} ]\nexists and that the files are not of size 0.")
kkonganti@0 307 }
kkonganti@0 308 }
kkonganti@0 309 else if (!file_path_obj.exists() || file_path_obj.size() == 0) {
kkonganti@0 310 stopNow("Please check if your ${msg} file\n" +
kkonganti@0 311 "[ ${file_path} ]\nexists and is not of size 0.")
kkonganti@0 312 }
kkonganti@0 313 }
kkonganti@0 314
kkonganti@0 315 /*
kkonganti@0 316 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0 317 HELP TEXT METHODS FOR BETTERCALLSAL WORKFLOW
kkonganti@0 318 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0 319 */
kkonganti@0 320
kkonganti@0 321 def help() {
kkonganti@0 322
kkonganti@0 323 Map helptext = [:]
kkonganti@0 324
kkonganti@0 325 helptext.putAll (
kkonganti@0 326 fastqEntryPointHelp() +
kkonganti@0 327 fastpHelp(params).text +
kkonganti@0 328 kmaalignHelp(params).text +
kkonganti@0 329 seqkitgrepHelp(params).text +
kkonganti@0 330 salmonidxHelp(params).text +
kkonganti@0 331 sourmashsketchHelp(params).text +
kkonganti@0 332 sourmashgatherHelp(params).text +
kkonganti@0 333 sfhpyHelp(params).text +
kkonganti@0 334 gsalkronapyHelp(params).text +
kkonganti@0 335 kronaktimporttextHelp(params).text +
kkonganti@0 336 wrapUpHelp()
kkonganti@0 337 )
kkonganti@0 338
kkonganti@0 339 return addPadding(helptext)
kkonganti@0 340 }