Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.2.1/workflows/centriflaken_hy.nf @ 47:30191f39a957

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"planemo upload"
author kkonganti
date Mon, 11 Jul 2022 12:19:48 -0400
parents 77494b0fa3c7
children
comparison
equal deleted inserted replaced
46:0dd0ebe5cddf 47:30191f39a957
106 .versions 106 .versions
107 .set { software_versions } 107 .set { software_versions }
108 108
109 FASTQC ( ch_processed_reads ) 109 FASTQC ( ch_processed_reads )
110 110
111 CENTRIFUGE_CLASSIFY( ch_processed_reads ) 111 CENTRIFUGE_CLASSIFY ( ch_processed_reads )
112 112
113 CENTRIFUGE_PROCESS( 113 CENTRIFUGE_PROCESS (
114 CENTRIFUGE_CLASSIFY.out.report 114 CENTRIFUGE_CLASSIFY.out.report
115 .join( CENTRIFUGE_CLASSIFY.out.output ) 115 .join( CENTRIFUGE_CLASSIFY.out.output )
116 ) 116 )
117 117
118 ch_processed_reads.join( CENTRIFUGE_PROCESS.out.extracted ) 118 ch_processed_reads.join ( CENTRIFUGE_PROCESS.out.extracted )
119 .set { ch_centrifuge_extracted } 119 .set { ch_centrifuge_extracted }
120 120
121 SEQKIT_GREP ( ch_centrifuge_extracted ) 121 SEQKIT_GREP ( ch_centrifuge_extracted )
122 122
123 // As of 06/02/2022, with the upcoming newer versions of NextFlow, we will be able to do 123 // As of 06/02/2022, with the upcoming newer versions of NextFlow, we will be able to do
143 } 143 }
144 .set { ch_spades_assembly } 144 .set { ch_spades_assembly }
145 145
146 ch_spades_assembly.ifEmpty { [ false, false ] } 146 ch_spades_assembly.ifEmpty { [ false, false ] }
147 147
148 KRAKEN2_CLASSIFY( ch_spades_assembly ) 148 KRAKEN2_CLASSIFY ( ch_spades_assembly )
149 149
150 KRAKEN2_EXTRACT_CONTIGS ( 150 KRAKEN2_EXTRACT_CONTIGS (
151 ch_spades_assembly 151 ch_spades_assembly
152 .join( KRAKEN2_CLASSIFY.out.kraken_output ), 152 .join( KRAKEN2_CLASSIFY.out.kraken_output ),
153 params.kraken2_extract_bug 153 params.kraken2_extract_bug
225 ) 225 )
226 .groupTuple(by: [0]) 226 .groupTuple(by: [0])
227 .map { it -> [ it[0], it[1].flatten() ]} 227 .map { it -> [ it[0], it[1].flatten() ]}
228 .set { ch_mqc_custom_tbl } 228 .set { ch_mqc_custom_tbl }
229 229
230 TABLE_SUMMARY( ch_mqc_custom_tbl ) 230 TABLE_SUMMARY ( ch_mqc_custom_tbl )
231 231
232 DUMP_SOFTWARE_VERSIONS ( 232 DUMP_SOFTWARE_VERSIONS (
233 software_versions 233 software_versions
234 .mix ( 234 .mix (
235 FASTQC.out.versions, 235 FASTQC.out.versions,
258 TABLE_SUMMARY.out.mqc_yml 258 TABLE_SUMMARY.out.mqc_yml
259 ) 259 )
260 .collect() 260 .collect()
261 .set { ch_multiqc } 261 .set { ch_multiqc }
262 262
263 MULTIQC( ch_multiqc ) 263 MULTIQC ( ch_multiqc )
264 } 264 }
265 265
266 /* 266 /*
267 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 267 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
268 ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG 268 ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG
320 320
321 def help() { 321 def help() {
322 322
323 Map helptext = [:] 323 Map helptext = [:]
324 324
325 helptext.putAll( 325 helptext.putAll (
326 fastqEntryPointHelp() + 326 fastqEntryPointHelp() +
327 kraken2Help(params).text + 327 kraken2Help(params).text +
328 centrifugeHelp(params).text + 328 centrifugeHelp(params).text +
329 spadesHelp(params).text + 329 spadesHelp(params).text +
330 serotypefinderHelp(params).text + 330 serotypefinderHelp(params).text +