Mercurial > repos > kkonganti > cfsan_bettercallsal

annotate 0.6.1/workflows/conf/process/bettercallsal.process.config @ 11:749faef1caa9

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"planemo upload"
author kkonganti
date Tue, 05 Sep 2023 11:51:40 -0400
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kkonganti@11 1 process {
kkonganti@11 2 withName: 'SEQKIT_SEQ' {
kkonganti@11 3 ext.args = [
kkonganti@11 4 params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
kkonganti@11 5 ].join(' ').trim()
kkonganti@11 6 }
kkonganti@11 7
kkonganti@11 8 if (params.bbmerge_run) {
kkonganti@11 9 withName: 'BBTOOLS_BBMERGE' {
kkonganti@11 10 ext.args = addParamsToSummary(
kkonganti@11 11 loadThisFunction("${params.toolshelp}${params.fs}bbmerge.nf").bbmergeHelp(params).helpparams
kkonganti@11 12 )
kkonganti@11 13 }
kkonganti@11 14 }
kkonganti@11 15
kkonganti@11 16 if (params.fastp_run) {
kkonganti@11 17 withName: 'FASTP' {
kkonganti@11 18 ext.args = addParamsToSummary(
kkonganti@11 19 loadThisFunction("${params.toolshelp}${params.fs}fastp.nf").fastpHelp(params).helpparams
kkonganti@11 20 )
kkonganti@11 21 }
kkonganti@11 22 }
kkonganti@11 23
kkonganti@11 24 if (params.bcs_concat_pe) {
kkonganti@11 25 withName: 'CAT_CAT' {
kkonganti@11 26 ext.prefix = 'concat.fastq.gz'
kkonganti@11 27 }
kkonganti@11 28 }
kkonganti@11 29
kkonganti@11 30
kkonganti@11 31 if (params.mashscreen_run) {
kkonganti@11 32 withName: 'MASH_SCREEN' {
kkonganti@11 33 ext.args = addParamsToSummary(
kkonganti@11 34 loadThisFunction("${params.toolshelp}${params.fs}mashscreen.nf").mashscreenHelp(params).helpparams
kkonganti@11 35 )
kkonganti@11 36 }
kkonganti@11 37 }
kkonganti@11 38
kkonganti@11 39 if (params.tuspy_run) {
kkonganti@11 40 withName: 'TOP_UNIQUE_SEROVARS' {
kkonganti@11 41 ext.args = addParamsToSummary(
kkonganti@11 42 loadThisFunction("${params.toolshelp}${params.fs}tuspy.nf").tuspyHelp(params).helpparams
kkonganti@11 43 )
kkonganti@11 44 }
kkonganti@11 45 }
kkonganti@11 46
kkonganti@11 47 if (params.gsrpy_run) {
kkonganti@11 48 withName: 'BCS_RESULTS' {
kkonganti@11 49 ext.args = addParamsToSummary(
kkonganti@11 50 loadThisFunction("${params.toolshelp}${params.fs}gsrpy.nf").gsrpyHelp(params).helpparams
kkonganti@11 51 )
kkonganti@11 52 }
kkonganti@11 53 }
kkonganti@11 54
kkonganti@11 55 if (params.sourmashsketch_run) {
kkonganti@11 56 withName: 'SOURMASH_SKETCH' {
kkonganti@11 57 ext.args = addParamsToSummary(
kkonganti@11 58 loadThisFunction("${params.toolshelp}${params.fs}sourmashsketch.nf").sourmashsketchHelp(params).helpparams
kkonganti@11 59 )
kkonganti@11 60 }
kkonganti@11 61 }
kkonganti@11 62
kkonganti@11 63 if (params.sourmashgather_run) {
kkonganti@11 64 withName: 'SOURMASH_GATHER' {
kkonganti@11 65 ext.args = addParamsToSummary(
kkonganti@11 66 loadThisFunction("${params.toolshelp}${params.fs}sourmashgather.nf").sourmashgatherHelp(params).helpparams
kkonganti@11 67 )
kkonganti@11 68
kkonganti@11 69 if (params.sfhpy_run) {
kkonganti@11 70 ext.args2 = addParamsToSummary(
kkonganti@11 71 loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
kkonganti@11 72 )
kkonganti@11 73 }
kkonganti@11 74 }
kkonganti@11 75 }
kkonganti@11 76
kkonganti@11 77 if (params.sourmashsearch_run) {
kkonganti@11 78 withName: 'SOURMASH_SEARCH' {
kkonganti@11 79 ext.args = addParamsToSummary(
kkonganti@11 80 loadThisFunction("${params.toolshelp}${params.fs}sourmashsearch.nf").sourmashsearchHelp(params).helpparams
kkonganti@11 81 )
kkonganti@11 82
kkonganti@11 83 if (params.sfhpy_run) {
kkonganti@11 84 ext.args2 = addParamsToSummary(
kkonganti@11 85 loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
kkonganti@11 86 )
kkonganti@11 87 }
kkonganti@11 88 }
kkonganti@11 89 }
kkonganti@11 90
kkonganti@11 91 if (params.kmaindex_run) {
kkonganti@11 92 withName: 'KMA_INDEX' {
kkonganti@11 93 ext.args = addParamsToSummary(
kkonganti@11 94 loadThisFunction("${params.toolshelp}${params.fs}kmaindex.nf").kmaindexHelp(params).helpparams
kkonganti@11 95 )
kkonganti@11 96 }
kkonganti@11 97 }
kkonganti@11 98
kkonganti@11 99 if (params.kmaalign_run) {
kkonganti@11 100 withName: 'KMA_ALIGN' {
kkonganti@11 101 ext.args = addParamsToSummary(
kkonganti@11 102 loadThisFunction("${params.toolshelp}${params.fs}kmaalign.nf").kmaalignHelp(params).helpparams
kkonganti@11 103 )
kkonganti@11 104 }
kkonganti@11 105 }
kkonganti@11 106
kkonganti@11 107 if (params.megahit_run) {
kkonganti@11 108 withName: 'MEGAHIT_ASSEMBLE' {
kkonganti@11 109 errorStrategy = 'ignore'
kkonganti@11 110 ext.args = addParamsToSummary(
kkonganti@11 111 loadThisFunction("${params.toolshelp}${params.fs}megahit.nf").megahitHelp(params).helpparams
kkonganti@11 112 )
kkonganti@11 113 }
kkonganti@11 114
kkonganti@11 115 withName: 'MLST' {
kkonganti@11 116 ext.when = params.mlst_run
kkonganti@11 117 ext.args = addParamsToSummary(
kkonganti@11 118 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
kkonganti@11 119 )
kkonganti@11 120 }
kkonganti@11 121
kkonganti@11 122 withName: 'ABRICATE_RUN' {
kkonganti@11 123 ext.when = params.abricate_run
kkonganti@11 124 ext.args = addParamsToSummary(
kkonganti@11 125 loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
kkonganti@11 126 )
kkonganti@11 127 }
kkonganti@11 128
kkonganti@11 129 withName: 'ABRICATE_SUMMARY' {
kkonganti@11 130 ext.when = params.abricate_summary_run
kkonganti@11 131 }
kkonganti@11 132 }
kkonganti@11 133
kkonganti@11 134 if (params.salmonidx_run){
kkonganti@11 135 withName: 'SALMON_INDEX' {
kkonganti@11 136 ext.args = addParamsToSummary(
kkonganti@11 137 loadThisFunction("${params.toolshelp}${params.fs}salmonidx.nf").salmonidxHelp(params).helpparams
kkonganti@11 138 )
kkonganti@11 139 }
kkonganti@11 140 }
kkonganti@11 141
kkonganti@11 142 withName: 'OTF_GENOME' {
kkonganti@11 143 errorStrategy = 'ignore'
kkonganti@11 144 }
kkonganti@11 145
kkonganti@11 146 }
kkonganti@11 147
kkonganti@11 148
kkonganti@11 149 // Parse the default params
kkonganti@11 150 def loadThisFunction (func_file) {
kkonganti@11 151 GroovyShell grvy_sh = new GroovyShell()
kkonganti@11 152 def func = grvy_sh.parse(new File ( func_file ) )
kkonganti@11 153 return func
kkonganti@11 154 }
kkonganti@11 155
kkonganti@11 156 // Method to add relevant final parameters to summary log
kkonganti@11 157 def addParamsToSummary(Map params_to_add = [:]) {
kkonganti@11 158
kkonganti@11 159 if (!params_to_add.isEmpty()) {
kkonganti@11 160 def not_null_params_to_add = params_to_add.findAll {
kkonganti@11 161 it.value.clivalue != null &&
kkonganti@11 162 it.value.clivalue != '[:]' &&
kkonganti@11 163 it.value.clivalue != ''
kkonganti@11 164 }
kkonganti@11 165
kkonganti@11 166 params.logtheseparams += not_null_params_to_add.keySet().toList()
kkonganti@11 167
kkonganti@11 168 return not_null_params_to_add.collect {
kkonganti@11 169 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
kkonganti@11 170 }.join(' ').trim()
kkonganti@11 171 }
kkonganti@11 172 return 1
kkonganti@11 173 }