Mercurial > repos > kkonganti > cfsan_centriflaken

annotate 0.4.2/workflows/conf/process/centriflaken_hy.process.config @ 143:620bffa66bbb tip

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planemo upload
author kkonganti
date Thu, 11 Jul 2024 14:48:07 -0400
parents 52045ea4679d
children
rev   line source
kkonganti@105 1 process {
kkonganti@105 2 withName: 'SEQKIT_SEQ' {
kkonganti@105 3 ext.args = [
kkonganti@105 4 params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
kkonganti@105 5 ].join(' ').trim()
kkonganti@105 6 }
kkonganti@105 7
kkonganti@105 8 if (params.seqkit_rmdup_run) {
kkonganti@105 9 withName: 'SEQKIT_RMDUP' {
kkonganti@105 10 ext.when = params.seqkit_rmdup_run
kkonganti@105 11 ext.args = addParamsToSummary(
kkonganti@105 12 loadThisFunction("${params.toolshelp}${params.fs}seqkitrmdup.nf").seqkitrmdupHelp(params).helpparams
kkonganti@105 13 )
kkonganti@105 14 }
kkonganti@105 15 }
kkonganti@105 16
kkonganti@105 17 if (params.seqkit_grep_on) {
kkonganti@105 18 withName: 'SEQKIT_GREP' {
kkonganti@105 19 ext.args = addParamsToSummary(
kkonganti@105 20 loadThisFunction("${params.toolshelp}${params.fs}seqkitgrep.nf").seqkitgrepHelp(params).helpparams
kkonganti@105 21 )
kkonganti@105 22 }
kkonganti@105 23 }
kkonganti@105 24
kkonganti@105 25 withName: 'CENTRIFUGE_CLASSIFY' {
kkonganti@105 26 ext.args = addParamsToSummary(
kkonganti@105 27 loadThisFunction("${params.toolshelp}${params.fs}centrifuge.nf").centrifugeHelp(params).helpparams
kkonganti@105 28 )
kkonganti@105 29 }
kkonganti@105 30
kkonganti@105 31 withName: 'KRAKEN2_CLASSIFY' {
kkonganti@105 32 ext.args = addParamsToSummary(
kkonganti@105 33 loadThisFunction("${params.toolshelp}${params.fs}kraken2.nf").kraken2Help(params).helpparams
kkonganti@105 34 )
kkonganti@105 35 }
kkonganti@105 36
kkonganti@105 37 withName: 'MEGAHIT_ASSEMBLE' {
kkonganti@105 38 ext.when = params.megahit_run
kkonganti@105 39 errorStrategy = 'ignore'
kkonganti@105 40 ext.args = addParamsToSummary(
kkonganti@105 41 loadThisFunction("${params.toolshelp}${params.fs}megahit.nf").megahitHelp(params).helpparams
kkonganti@105 42 )
kkonganti@105 43 }
kkonganti@105 44
kkonganti@105 45 withName: 'SPADES_ASSEMBLE' {
kkonganti@105 46 ext.when = params.spades_run
kkonganti@105 47 errorStrategy = 'ignore'
kkonganti@105 48 ext.args = addParamsToSummary(
kkonganti@105 49 loadThisFunction("${params.toolshelp}${params.fs}spades.nf").spadesHelp(params).helpparams
kkonganti@105 50 )
kkonganti@105 51 }
kkonganti@105 52
kkonganti@105 53 if (params.ectyper_run) {
kkonganti@105 54 withName: 'ECTYPER' {
kkonganti@105 55 ext.when = params.ectyper_run
kkonganti@105 56 ext.args = addParamsToSummary(
kkonganti@105 57 loadThisFunction("${params.toolshelp}${params.fs}ectyper.nf").ectyperHelp(params).helpparams
kkonganti@105 58 )
kkonganti@105 59 }
kkonganti@105 60 }
kkonganti@105 61
kkonganti@105 62 withName: 'SEROTYPEFINDER' {
kkonganti@105 63 ext.when = params.serotypefinder_run
kkonganti@105 64 ext.args = addParamsToSummary(
kkonganti@105 65 loadThisFunction("${params.toolshelp}${params.fs}serotypefinder.nf").serotypefinderHelp(params).helpparams
kkonganti@105 66 )
kkonganti@105 67 }
kkonganti@105 68
kkonganti@105 69 withName: 'SEQSERO2' {
kkonganti@105 70 ext.when = params.seqsero2_run
kkonganti@105 71 ext.args = addParamsToSummary(
kkonganti@105 72 loadThisFunction("${params.toolshelp}${params.fs}seqsero2.nf").seqsero2Help(params).helpparams
kkonganti@105 73 )
kkonganti@105 74 }
kkonganti@105 75
kkonganti@105 76 withName: 'MLST' {
kkonganti@105 77 ext.when = params.mlst_run
kkonganti@105 78 ext.args = addParamsToSummary(
kkonganti@105 79 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
kkonganti@105 80 )
kkonganti@105 81 }
kkonganti@105 82
kkonganti@105 83 if (params.amrfinderplus_run) {
kkonganti@105 84 withName: 'AMRFINDERPLUS_RUN' {
kkonganti@105 85 ext.when = params.amrfinderplus_run
kkonganti@105 86 ext.args = addParamsToSummary(
kkonganti@105 87 loadThisFunction("${params.toolshelp}${params.fs}amrfinderplus.nf").amrfinderplusHelp(params).helpparams
kkonganti@105 88 )
kkonganti@105 89 }
kkonganti@105 90 }
kkonganti@105 91
kkonganti@105 92 withName: 'ABRICATE_RUN' {
kkonganti@105 93 ext.when = params.abricate_run
kkonganti@105 94 ext.args = addParamsToSummary(
kkonganti@105 95 loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
kkonganti@105 96 )
kkonganti@105 97 }
kkonganti@105 98
kkonganti@105 99 withName: 'ABRICATE_SUMMARY' {
kkonganti@105 100 ext.when = params.abricate_summary_run
kkonganti@105 101 }
kkonganti@105 102 }
kkonganti@105 103
kkonganti@105 104 // Method to instantiate a new function parser
kkonganti@105 105 // Need to refactor using ScriptParser... another day
kkonganti@105 106 def loadThisFunction (func_file) {
kkonganti@105 107 GroovyShell grvy_sh = new GroovyShell()
kkonganti@105 108 def func = grvy_sh.parse(new File ( func_file ) )
kkonganti@105 109 return func
kkonganti@105 110 }
kkonganti@105 111
kkonganti@105 112 // Method to add relevant final parameters to summary log
kkonganti@105 113 def addParamsToSummary(Map params_to_add = [:]) {
kkonganti@105 114
kkonganti@105 115 if (!params_to_add.isEmpty()) {
kkonganti@105 116 def not_null_params_to_add = params_to_add.findAll {
kkonganti@105 117 it.value.clivalue != null &&
kkonganti@105 118 it.value.clivalue != '[:]' &&
kkonganti@105 119 it.value.clivalue != ''
kkonganti@105 120 }
kkonganti@105 121
kkonganti@105 122 params.logtheseparams += not_null_params_to_add.keySet().toList()
kkonganti@105 123
kkonganti@105 124 return not_null_params_to_add.collect {
kkonganti@105 125 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
kkonganti@105 126 }.join(' ').trim()
kkonganti@105 127 }
kkonganti@105 128 return 1
kkonganti@105 129 }