Mercurial > repos > kkonganti > cfsan_bettercallsal

annotate 0.7.0/workflows/conf/process/bettercallsal.process.config @ 21:4ce0e079377d tip

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planemo upload
author kkonganti
date Mon, 15 Jul 2024 12:01:00 -0400
parents 0e7a0053e4a6
children
rev   line source
kkonganti@17 1 process {
kkonganti@17 2 withName: 'SEQKIT_SEQ' {
kkonganti@17 3 ext.args = [
kkonganti@17 4 params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
kkonganti@17 5 ].join(' ').trim()
kkonganti@17 6 }
kkonganti@17 7
kkonganti@17 8 if (params.bbmerge_run) {
kkonganti@17 9 withName: 'BBTOOLS_BBMERGE' {
kkonganti@17 10 ext.args = addParamsToSummary(
kkonganti@17 11 loadThisFunction("${params.toolshelp}${params.fs}bbmerge.nf").bbmergeHelp(params).helpparams
kkonganti@17 12 )
kkonganti@17 13 }
kkonganti@17 14 }
kkonganti@17 15
kkonganti@17 16 if (params.fastp_run) {
kkonganti@17 17 withName: 'FASTP' {
kkonganti@17 18 ext.args = addParamsToSummary(
kkonganti@17 19 loadThisFunction("${params.toolshelp}${params.fs}fastp.nf").fastpHelp(params).helpparams
kkonganti@17 20 )
kkonganti@17 21 }
kkonganti@17 22 }
kkonganti@17 23
kkonganti@17 24 if (params.bcs_concat_pe) {
kkonganti@17 25 withName: 'CAT_CAT' {
kkonganti@17 26 ext.prefix = 'concat.fastq.gz'
kkonganti@17 27 }
kkonganti@17 28 }
kkonganti@17 29
kkonganti@17 30
kkonganti@17 31 if (params.mashscreen_run) {
kkonganti@17 32 withName: 'MASH_SCREEN' {
kkonganti@17 33 ext.args = addParamsToSummary(
kkonganti@17 34 loadThisFunction("${params.toolshelp}${params.fs}mashscreen.nf").mashscreenHelp(params).helpparams
kkonganti@17 35 )
kkonganti@17 36 }
kkonganti@17 37 }
kkonganti@17 38
kkonganti@17 39 if (params.tuspy_run) {
kkonganti@17 40 withName: 'TOP_UNIQUE_SEROVARS' {
kkonganti@17 41 ext.args = addParamsToSummary(
kkonganti@17 42 loadThisFunction("${params.toolshelp}${params.fs}tuspy.nf").tuspyHelp(params).helpparams
kkonganti@17 43 )
kkonganti@17 44 }
kkonganti@17 45 }
kkonganti@17 46
kkonganti@17 47 if (params.gsrpy_run) {
kkonganti@17 48 withName: 'BCS_RESULTS' {
kkonganti@17 49 ext.args = addParamsToSummary(
kkonganti@17 50 loadThisFunction("${params.toolshelp}${params.fs}gsrpy.nf").gsrpyHelp(params).helpparams
kkonganti@17 51 )
kkonganti@17 52 }
kkonganti@17 53 }
kkonganti@17 54
kkonganti@17 55 if (params.sourmashsketch_run) {
kkonganti@17 56 withName: 'SOURMASH_SKETCH' {
kkonganti@17 57 ext.args = addParamsToSummary(
kkonganti@17 58 loadThisFunction("${params.toolshelp}${params.fs}sourmashsketch.nf").sourmashsketchHelp(params).helpparams
kkonganti@17 59 )
kkonganti@17 60 }
kkonganti@17 61 }
kkonganti@17 62
kkonganti@17 63 if (params.sourmashgather_run) {
kkonganti@17 64 withName: 'SOURMASH_GATHER' {
kkonganti@17 65 ext.args = addParamsToSummary(
kkonganti@17 66 loadThisFunction("${params.toolshelp}${params.fs}sourmashgather.nf").sourmashgatherHelp(params).helpparams
kkonganti@17 67 )
kkonganti@17 68
kkonganti@17 69 if (params.sfhpy_run) {
kkonganti@17 70 ext.args2 = addParamsToSummary(
kkonganti@17 71 loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
kkonganti@17 72 )
kkonganti@17 73 }
kkonganti@17 74 }
kkonganti@17 75 }
kkonganti@17 76
kkonganti@17 77 if (params.sourmashsearch_run) {
kkonganti@17 78 withName: 'SOURMASH_SEARCH' {
kkonganti@17 79 ext.args = addParamsToSummary(
kkonganti@17 80 loadThisFunction("${params.toolshelp}${params.fs}sourmashsearch.nf").sourmashsearchHelp(params).helpparams
kkonganti@17 81 )
kkonganti@17 82
kkonganti@17 83 if (params.sfhpy_run) {
kkonganti@17 84 ext.args2 = addParamsToSummary(
kkonganti@17 85 loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
kkonganti@17 86 )
kkonganti@17 87 }
kkonganti@17 88 }
kkonganti@17 89 }
kkonganti@17 90
kkonganti@17 91 if (params.kmaindex_run) {
kkonganti@17 92 withName: 'KMA_INDEX' {
kkonganti@17 93 ext.args = addParamsToSummary(
kkonganti@17 94 loadThisFunction("${params.toolshelp}${params.fs}kmaindex.nf").kmaindexHelp(params).helpparams
kkonganti@17 95 )
kkonganti@17 96 }
kkonganti@17 97 }
kkonganti@17 98
kkonganti@17 99 if (params.kmaalign_run) {
kkonganti@17 100 withName: 'KMA_ALIGN' {
kkonganti@17 101 ext.args = addParamsToSummary(
kkonganti@17 102 loadThisFunction("${params.toolshelp}${params.fs}kmaalign.nf").kmaalignHelp(params).helpparams
kkonganti@17 103 )
kkonganti@17 104 }
kkonganti@17 105 }
kkonganti@17 106
kkonganti@17 107 if (params.megahit_run) {
kkonganti@17 108 withName: 'MEGAHIT_ASSEMBLE' {
kkonganti@17 109 errorStrategy = 'ignore'
kkonganti@17 110 ext.args = addParamsToSummary(
kkonganti@17 111 loadThisFunction("${params.toolshelp}${params.fs}megahit.nf").megahitHelp(params).helpparams
kkonganti@17 112 )
kkonganti@17 113 }
kkonganti@17 114
kkonganti@17 115 withName: 'MLST' {
kkonganti@17 116 ext.when = params.mlst_run
kkonganti@17 117 ext.args = addParamsToSummary(
kkonganti@17 118 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
kkonganti@17 119 )
kkonganti@17 120 }
kkonganti@17 121
kkonganti@17 122 withName: 'ABRICATE_RUN' {
kkonganti@17 123 ext.when = params.abricate_run
kkonganti@17 124 ext.args = addParamsToSummary(
kkonganti@17 125 loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
kkonganti@17 126 )
kkonganti@17 127 }
kkonganti@17 128
kkonganti@17 129 withName: 'ABRICATE_SUMMARY' {
kkonganti@17 130 ext.when = params.abricate_summary_run
kkonganti@17 131 }
kkonganti@17 132 }
kkonganti@17 133
kkonganti@17 134 if (params.salmonidx_run){
kkonganti@17 135 withName: 'SALMON_INDEX' {
kkonganti@17 136 ext.args = addParamsToSummary(
kkonganti@17 137 loadThisFunction("${params.toolshelp}${params.fs}salmonidx.nf").salmonidxHelp(params).helpparams
kkonganti@17 138 )
kkonganti@17 139 }
kkonganti@17 140 }
kkonganti@17 141
kkonganti@17 142 withName: 'OTF_GENOME' {
kkonganti@17 143 errorStrategy = 'ignore'
kkonganti@17 144 }
kkonganti@17 145
kkonganti@17 146 }
kkonganti@17 147
kkonganti@17 148
kkonganti@17 149 // Parse the default params
kkonganti@17 150 def loadThisFunction (func_file) {
kkonganti@17 151 GroovyShell grvy_sh = new GroovyShell()
kkonganti@17 152 def func = grvy_sh.parse(new File ( func_file ) )
kkonganti@17 153 return func
kkonganti@17 154 }
kkonganti@17 155
kkonganti@17 156 // Method to add relevant final parameters to summary log
kkonganti@17 157 def addParamsToSummary(Map params_to_add = [:]) {
kkonganti@17 158
kkonganti@17 159 if (!params_to_add.isEmpty()) {
kkonganti@17 160 def not_null_params_to_add = params_to_add.findAll {
kkonganti@17 161 it.value.clivalue != null &&
kkonganti@17 162 it.value.clivalue != '[:]' &&
kkonganti@17 163 it.value.clivalue != ''
kkonganti@17 164 }
kkonganti@17 165
kkonganti@17 166 params.logtheseparams += not_null_params_to_add.keySet().toList()
kkonganti@17 167
kkonganti@17 168 return not_null_params_to_add.collect {
kkonganti@17 169 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
kkonganti@17 170 }.join(' ').trim()
kkonganti@17 171 }
kkonganti@17 172 return 1
kkonganti@17 173 }