Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 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
comparison
equal deleted inserted replaced
46:0dd0ebe5cddf 47:30191f39a957
105 .versions 105 .versions
106 .set { software_versions } 106 .set { software_versions }
107 107
108 FASTQC ( ch_processed_reads ) 108 FASTQC ( ch_processed_reads )
109 109
110 CENTRIFUGE_CLASSIFY( ch_processed_reads ) 110 CENTRIFUGE_CLASSIFY ( ch_processed_reads )
111 111
112 CENTRIFUGE_PROCESS( 112 CENTRIFUGE_PROCESS (
113 CENTRIFUGE_CLASSIFY.out.report 113 CENTRIFUGE_CLASSIFY.out.report
114 .join( CENTRIFUGE_CLASSIFY.out.output ) 114 .join( CENTRIFUGE_CLASSIFY.out.output )
115 ) 115 )
116 116
117 ch_processed_reads.join( CENTRIFUGE_PROCESS.out.extracted ) 117 ch_processed_reads.join ( CENTRIFUGE_PROCESS.out.extracted )
118 .set { ch_centrifuge_extracted } 118 .set { ch_centrifuge_extracted }
119 119
120 SEQKIT_GREP ( ch_centrifuge_extracted ) 120 SEQKIT_GREP ( ch_centrifuge_extracted )
121 121
122 FLYE_ASSEMBLE ( SEQKIT_GREP.out.fastx ) 122 FLYE_ASSEMBLE ( SEQKIT_GREP.out.fastx )
126 .assembly 126 .assembly
127 .set { ch_flye_assembly } 127 .set { ch_flye_assembly }
128 128
129 ch_flye_assembly.ifEmpty { [ false, false ] } 129 ch_flye_assembly.ifEmpty { [ false, false ] }
130 130
131 KRAKEN2_CLASSIFY( ch_flye_assembly ) 131 KRAKEN2_CLASSIFY ( ch_flye_assembly )
132 132
133 KRAKEN2_EXTRACT_CONTIGS ( 133 KRAKEN2_EXTRACT_CONTIGS (
134 ch_flye_assembly 134 ch_flye_assembly
135 .join( KRAKEN2_CLASSIFY.out.kraken_output ), 135 .join( KRAKEN2_CLASSIFY.out.kraken_output ),
136 params.kraken2_extract_bug 136 params.kraken2_extract_bug
211 ) 211 )
212 .groupTuple(by: [0]) 212 .groupTuple(by: [0])
213 .map { it -> [ it[0], it[1].flatten() ]} 213 .map { it -> [ it[0], it[1].flatten() ]}
214 .set { ch_mqc_custom_tbl } 214 .set { ch_mqc_custom_tbl }
215 215
216 TABLE_SUMMARY( ch_mqc_custom_tbl ) 216 TABLE_SUMMARY ( ch_mqc_custom_tbl )
217 217
218 DUMP_SOFTWARE_VERSIONS ( 218 DUMP_SOFTWARE_VERSIONS (
219 software_versions 219 software_versions
220 .mix ( 220 .mix (
221 FASTQC.out.versions, 221 FASTQC.out.versions,
244 TABLE_SUMMARY.out.mqc_yml 244 TABLE_SUMMARY.out.mqc_yml
245 ) 245 )
246 .collect() 246 .collect()
247 .set { ch_multiqc } 247 .set { ch_multiqc }
248 248
249 MULTIQC( ch_multiqc ) 249 MULTIQC ( ch_multiqc )
250 } 250 }
251 251
252 /* 252 /*
253 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 253 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
254 ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG 254 ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG
306 306
307 def help() { 307 def help() {
308 308
309 Map helptext = [:] 309 Map helptext = [:]
310 310
311 helptext.putAll( 311 helptext.putAll (
312 fastqEntryPointHelp() + 312 fastqEntryPointHelp() +
313 kraken2Help(params).text + 313 kraken2Help(params).text +
314 centrifugeHelp(params).text + 314 centrifugeHelp(params).text +
315 flyeHelp(params).text + 315 flyeHelp(params).text +
316 serotypefinderHelp(params).text + 316 serotypefinderHelp(params).text +