Mercurial > repos > kkonganti > cfsan_cronology

annotate 0.1.0/workflows/conf/process/cronology.process.config @ 0:c8597e9e1a97

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"planemo upload"
author kkonganti
date Mon, 27 Nov 2023 12:37:44 -0500
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kkonganti@0 1 process {
kkonganti@0 2 withName: 'SEQKIT_SEQ' {
kkonganti@0 3 ext.args = [
kkonganti@0 4 params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
kkonganti@0 5 ].join(' ').trim()
kkonganti@0 6 }
kkonganti@0 7
kkonganti@0 8 if (params.dpubmlstpy_run) {
kkonganti@0 9 withName: 'DOWNLOAD_PUBMLST_SCHEME' {
kkonganti@0 10 ext.args = addParamsToSummary(
kkonganti@0 11 loadThisFunction("${params.toolshelp}${params.fs}dpubmlstpy.nf").dpubmlstpyHelp(params).helpparams
kkonganti@0 12 )
kkonganti@0 13 }
kkonganti@0 14 }
kkonganti@0 15
kkonganti@0 16 if (params.fastp_run) {
kkonganti@0 17 withName: 'FASTP' {
kkonganti@0 18 ext.args = addParamsToSummary(
kkonganti@0 19 loadThisFunction("${params.toolshelp}${params.fs}fastp.nf").fastpHelp(params).helpparams
kkonganti@0 20 )
kkonganti@0 21 }
kkonganti@0 22 }
kkonganti@0 23
kkonganti@0 24 if (params.mashscreen_run) {
kkonganti@0 25 withName: 'MASH_SCREEN' {
kkonganti@0 26 ext.args = addParamsToSummary(
kkonganti@0 27 loadThisFunction("${params.toolshelp}${params.fs}mashscreen.nf").mashscreenHelp(params).helpparams
kkonganti@0 28 )
kkonganti@0 29 }
kkonganti@0 30 }
kkonganti@0 31
kkonganti@0 32 if (params.tuspy_run) {
kkonganti@0 33 withName: 'TOP_UNIQUE_SEROVARS' {
kkonganti@0 34 ext.args = addParamsToSummary(
kkonganti@0 35 loadThisFunction("${params.toolshelp}${params.fs}tuspy.nf").tuspyHelp(params).helpparams
kkonganti@0 36 )
kkonganti@0 37 }
kkonganti@0 38 }
kkonganti@0 39
kkonganti@0 40 if (params.spades_run) {
kkonganti@0 41 withName: 'SPADES_ASSEMBLE' {
kkonganti@0 42 errorStrategy = 'ignore'
kkonganti@0 43 ext.args = addParamsToSummary(
kkonganti@0 44 loadThisFunction("${params.toolshelp}${params.fs}spades.nf").spadesHelp(params).helpparams
kkonganti@0 45 )
kkonganti@0 46 }
kkonganti@0 47 }
kkonganti@0 48
kkonganti@0 49 if (params.shovill_run) {
kkonganti@0 50 withName: 'SHOVILL' {
kkonganti@0 51 errorStrategy = 'ignore'
kkonganti@0 52 ext.args = addParamsToSummary(
kkonganti@0 53 loadThisFunction("${params.toolshelp}${params.fs}shovill.nf").shovillHelp(params).helpparams
kkonganti@0 54 )
kkonganti@0 55 }
kkonganti@0 56 }
kkonganti@0 57
kkonganti@0 58 if (params.polypolish_run) {
kkonganti@0 59 withName: 'POLYPOLISH' {
kkonganti@0 60 ext.args = addParamsToSummary(
kkonganti@0 61 loadThisFunction("${params.toolshelp}${params.fs}polypolish.nf").polypolishHelp(params).helpparams
kkonganti@0 62 )
kkonganti@0 63 }
kkonganti@0 64 }
kkonganti@0 65
kkonganti@0 66 if (params.quast_run) {
kkonganti@0 67 withName: 'QUAST' {
kkonganti@0 68 ext.args = addParamsToSummary(
kkonganti@0 69 loadThisFunction("${params.toolshelp}${params.fs}quast.nf").quastHelp(params).helpparams
kkonganti@0 70 )
kkonganti@0 71 }
kkonganti@0 72 }
kkonganti@0 73
kkonganti@0 74 if (params.pirate_run) {
kkonganti@0 75 withName: 'PIRATE' {
kkonganti@0 76 ext.args = addParamsToSummary(
kkonganti@0 77 loadThisFunction("${params.toolshelp}${params.fs}pirate.nf").pirateHelp(params).helpparams
kkonganti@0 78 )
kkonganti@0 79 }
kkonganti@0 80 }
kkonganti@0 81
kkonganti@0 82 if (params.prodka_run) {
kkonganti@0 83 withName: 'PRODIGAL' {
kkonganti@0 84 ext.args = addParamsToSummary(
kkonganti@0 85 loadThisFunction("${params.toolshelp}${params.fs}prodigal.nf").prodigalHelp(params).helpparams
kkonganti@0 86 )
kkonganti@0 87 }
kkonganti@0 88
kkonganti@0 89 withName: 'PROKKA' {
kkonganti@0 90 ext.args = addParamsToSummary(
kkonganti@0 91 loadThisFunction("${params.toolshelp}${params.fs}prokka.nf").prokkaHelp(params).helpparams
kkonganti@0 92 )
kkonganti@0 93 }
kkonganti@0 94 }
kkonganti@0 95
kkonganti@0 96 if (params.mlst_run) {
kkonganti@0 97 withName: 'MLST' {
kkonganti@0 98 ext.args = addParamsToSummary(
kkonganti@0 99 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
kkonganti@0 100 )
kkonganti@0 101 }
kkonganti@0 102 }
kkonganti@0 103
kkonganti@0 104 if (params.abricate_run) {
kkonganti@0 105 withName: 'ABRICATE_RUN' {
kkonganti@0 106 ext.args = addParamsToSummary(
kkonganti@0 107 loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
kkonganti@0 108 )
kkonganti@0 109 }
kkonganti@0 110 }
kkonganti@0 111
kkonganti@0 112 if (params.mashtree_run) {
kkonganti@0 113 withName: 'MASHTREE' {
kkonganti@0 114 ext.args = addParamsToSummary(
kkonganti@0 115 loadThisFunction("${params.toolshelp}${params.fs}mashtree.nf").mashtreeHelp(params).helpparams
kkonganti@0 116 )
kkonganti@0 117 }
kkonganti@0 118 }
kkonganti@0 119 }
kkonganti@0 120
kkonganti@0 121 // Method to instantiate a new function parser
kkonganti@0 122 // Need to refactor using ScriptParser... another day
kkonganti@0 123 def loadThisFunction (func_file) {
kkonganti@0 124 GroovyShell grvy_sh = new GroovyShell()
kkonganti@0 125 def func = grvy_sh.parse(new File ( func_file ) )
kkonganti@0 126 return func
kkonganti@0 127 }
kkonganti@0 128
kkonganti@0 129 // Method to add relevant final parameters to summary log
kkonganti@0 130 def addParamsToSummary(Map params_to_add = [:]) {
kkonganti@0 131
kkonganti@0 132 if (!params_to_add.isEmpty()) {
kkonganti@0 133 def not_null_params_to_add = params_to_add.findAll {
kkonganti@0 134 it.value.clivalue != null &&
kkonganti@0 135 it.value.clivalue != '[:]' &&
kkonganti@0 136 it.value.clivalue != ''
kkonganti@0 137 }
kkonganti@0 138
kkonganti@0 139 params.logtheseparams += not_null_params_to_add.keySet().toList()
kkonganti@0 140
kkonganti@0 141 return not_null_params_to_add.collect {
kkonganti@0 142 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
kkonganti@0 143 }.join(' ').trim()
kkonganti@0 144 }
kkonganti@0 145 return 1
kkonganti@0 146 }