Mercurial > repos > kkonganti > cfsan_centriflaken

annotate 0.4.0/workflows/conf/process/centriflaken_hy.process.config @ 101:ce6d9548fe89

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"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
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kkonganti@101 1 process {
kkonganti@101 2 withName: 'SEQKIT_SEQ' {
kkonganti@101 3 ext.args = [
kkonganti@101 4 params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
kkonganti@101 5 ].join(' ').trim()
kkonganti@101 6 }
kkonganti@101 7
kkonganti@101 8 if (params.seqkit_rmdup_run) {
kkonganti@101 9 withName: 'SEQKIT_RMDUP' {
kkonganti@101 10 ext.when = params.seqkit_rmdup_run
kkonganti@101 11 ext.args = addParamsToSummary(
kkonganti@101 12 loadThisFunction("${params.toolshelp}${params.fs}seqkitrmdup.nf").seqkitrmdupHelp(params).helpparams
kkonganti@101 13 )
kkonganti@101 14 }
kkonganti@101 15 }
kkonganti@101 16
kkonganti@101 17 if (params.seqkit_grep_on) {
kkonganti@101 18 withName: 'SEQKIT_GREP' {
kkonganti@101 19 ext.args = addParamsToSummary(
kkonganti@101 20 loadThisFunction("${params.toolshelp}${params.fs}seqkitgrep.nf").seqkitgrepHelp(params).helpparams
kkonganti@101 21 )
kkonganti@101 22 }
kkonganti@101 23 }
kkonganti@101 24
kkonganti@101 25 withName: 'CENTRIFUGE_CLASSIFY' {
kkonganti@101 26 ext.args = addParamsToSummary(
kkonganti@101 27 loadThisFunction("${params.toolshelp}${params.fs}centrifuge.nf").centrifugeHelp(params).helpparams
kkonganti@101 28 )
kkonganti@101 29 }
kkonganti@101 30
kkonganti@101 31 withName: 'KRAKEN2_CLASSIFY' {
kkonganti@101 32 ext.args = addParamsToSummary(
kkonganti@101 33 loadThisFunction("${params.toolshelp}${params.fs}kraken2.nf").kraken2Help(params).helpparams
kkonganti@101 34 )
kkonganti@101 35 }
kkonganti@101 36
kkonganti@101 37 withName: 'MEGAHIT_ASSEMBLE' {
kkonganti@101 38 ext.when = params.megahit_run
kkonganti@101 39 errorStrategy = 'ignore'
kkonganti@101 40 ext.args = addParamsToSummary(
kkonganti@101 41 loadThisFunction("${params.toolshelp}${params.fs}megahit.nf").megahitHelp(params).helpparams
kkonganti@101 42 )
kkonganti@101 43 }
kkonganti@101 44
kkonganti@101 45 withName: 'SPADES_ASSEMBLE' {
kkonganti@101 46 ext.when = params.spades_run
kkonganti@101 47 errorStrategy = 'ignore'
kkonganti@101 48 ext.args = addParamsToSummary(
kkonganti@101 49 loadThisFunction("${params.toolshelp}${params.fs}spades.nf").spadesHelp(params).helpparams
kkonganti@101 50 )
kkonganti@101 51 }
kkonganti@101 52
kkonganti@101 53 if (params.ectyper_run) {
kkonganti@101 54 withName: 'ECTYPER' {
kkonganti@101 55 ext.when = params.ectyper_run
kkonganti@101 56 ext.args = addParamsToSummary(
kkonganti@101 57 loadThisFunction("${params.toolshelp}${params.fs}ectyper.nf").ectyperHelp(params).helpparams
kkonganti@101 58 )
kkonganti@101 59 }
kkonganti@101 60 }
kkonganti@101 61
kkonganti@101 62 withName: 'SEROTYPEFINDER' {
kkonganti@101 63 ext.when = params.serotypefinder_run
kkonganti@101 64 ext.args = addParamsToSummary(
kkonganti@101 65 loadThisFunction("${params.toolshelp}${params.fs}serotypefinder.nf").serotypefinderHelp(params).helpparams
kkonganti@101 66 )
kkonganti@101 67 }
kkonganti@101 68
kkonganti@101 69 withName: 'SEQSERO2' {
kkonganti@101 70 ext.when = params.seqsero2_run
kkonganti@101 71 ext.args = addParamsToSummary(
kkonganti@101 72 loadThisFunction("${params.toolshelp}${params.fs}seqsero2.nf").seqsero2Help(params).helpparams
kkonganti@101 73 )
kkonganti@101 74 }
kkonganti@101 75
kkonganti@101 76 withName: 'MLST' {
kkonganti@101 77 ext.when = params.mlst_run
kkonganti@101 78 ext.args = addParamsToSummary(
kkonganti@101 79 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
kkonganti@101 80 )
kkonganti@101 81 }
kkonganti@101 82
kkonganti@101 83 if (params.amrfinderplus_run) {
kkonganti@101 84 withName: 'AMRFINDERPLUS_RUN' {
kkonganti@101 85 ext.when = params.amrfinderplus_run
kkonganti@101 86 ext.args = addParamsToSummary(
kkonganti@101 87 loadThisFunction("${params.toolshelp}${params.fs}amrfinderplus.nf").amrfinderplusHelp(params).helpparams
kkonganti@101 88 )
kkonganti@101 89 }
kkonganti@101 90 }
kkonganti@101 91
kkonganti@101 92 withName: 'ABRICATE_RUN' {
kkonganti@101 93 ext.when = params.abricate_run
kkonganti@101 94 ext.args = addParamsToSummary(
kkonganti@101 95 loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
kkonganti@101 96 )
kkonganti@101 97 }
kkonganti@101 98
kkonganti@101 99 withName: 'ABRICATE_SUMMARY' {
kkonganti@101 100 ext.when = params.abricate_summary_run
kkonganti@101 101 }
kkonganti@101 102 }
kkonganti@101 103
kkonganti@101 104 // Method to instantiate a new function parser
kkonganti@101 105 // Need to refactor using ScriptParser... another day
kkonganti@101 106 def loadThisFunction (func_file) {
kkonganti@101 107 GroovyShell grvy_sh = new GroovyShell()
kkonganti@101 108 def func = grvy_sh.parse(new File ( func_file ) )
kkonganti@101 109 return func
kkonganti@101 110 }
kkonganti@101 111
kkonganti@101 112 // Method to add relevant final parameters to summary log
kkonganti@101 113 def addParamsToSummary(Map params_to_add = [:]) {
kkonganti@101 114
kkonganti@101 115 if (!params_to_add.isEmpty()) {
kkonganti@101 116 def not_null_params_to_add = params_to_add.findAll {
kkonganti@101 117 it.value.clivalue != null &&
kkonganti@101 118 it.value.clivalue != '[:]' &&
kkonganti@101 119 it.value.clivalue != ''
kkonganti@101 120 }
kkonganti@101 121
kkonganti@101 122 params.logtheseparams += not_null_params_to_add.keySet().toList()
kkonganti@101 123
kkonganti@101 124 return not_null_params_to_add.collect {
kkonganti@101 125 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
kkonganti@101 126 }.join(' ').trim()
kkonganti@101 127 }
kkonganti@101 128 return 1
kkonganti@101 129 }