Mercurial > repos > kkonganti > cfsan_bettercallsal

annotate 0.5.0/workflows/conf/process/bettercallsal.process.config @ 13:74baf1a6c3bd

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"planemo upload"
author kkonganti
date Tue, 05 Sep 2023 13:04:15 -0400
parents 365849f031fd
children
rev   line source
kkonganti@1 1 process {
kkonganti@1 2 withName: 'SEQKIT_SEQ' {
kkonganti@1 3 ext.args = [
kkonganti@1 4 params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
kkonganti@1 5 ].join(' ').trim()
kkonganti@1 6 }
kkonganti@1 7
kkonganti@1 8 if (params.bbmerge_run) {
kkonganti@1 9 withName: 'BBTOOLS_BBMERGE' {
kkonganti@1 10 ext.args = addParamsToSummary(
kkonganti@1 11 loadThisFunction("${params.toolshelp}${params.fs}bbmerge.nf").bbmergeHelp(params).helpparams
kkonganti@1 12 )
kkonganti@1 13 }
kkonganti@1 14 }
kkonganti@1 15
kkonganti@1 16 if (params.fastp_run) {
kkonganti@1 17 withName: 'FASTP' {
kkonganti@1 18 ext.args = addParamsToSummary(
kkonganti@1 19 loadThisFunction("${params.toolshelp}${params.fs}fastp.nf").fastpHelp(params).helpparams
kkonganti@1 20 )
kkonganti@1 21 }
kkonganti@1 22 }
kkonganti@1 23
kkonganti@1 24 if (params.bcs_concat_pe) {
kkonganti@1 25 withName: 'CAT_CAT' {
kkonganti@1 26 ext.prefix = 'concat.fastq.gz'
kkonganti@1 27 }
kkonganti@1 28 }
kkonganti@1 29
kkonganti@1 30
kkonganti@1 31 if (params.mashscreen_run) {
kkonganti@1 32 withName: 'MASH_SCREEN' {
kkonganti@1 33 ext.args = addParamsToSummary(
kkonganti@1 34 loadThisFunction("${params.toolshelp}${params.fs}mashscreen.nf").mashscreenHelp(params).helpparams
kkonganti@1 35 )
kkonganti@1 36 }
kkonganti@1 37 }
kkonganti@1 38
kkonganti@1 39 if (params.tuspy_run) {
kkonganti@1 40 withName: 'TOP_UNIQUE_SEROVARS' {
kkonganti@1 41 ext.args = addParamsToSummary(
kkonganti@1 42 loadThisFunction("${params.toolshelp}${params.fs}tuspy.nf").tuspyHelp(params).helpparams
kkonganti@1 43 )
kkonganti@1 44 }
kkonganti@1 45 }
kkonganti@1 46
kkonganti@1 47 if (params.gsrpy_run) {
kkonganti@1 48 withName: 'BCS_RESULTS' {
kkonganti@1 49 ext.args = addParamsToSummary(
kkonganti@1 50 loadThisFunction("${params.toolshelp}${params.fs}gsrpy.nf").gsrpyHelp(params).helpparams
kkonganti@1 51 )
kkonganti@1 52 }
kkonganti@1 53 }
kkonganti@1 54
kkonganti@1 55 if (params.sourmashsketch_run) {
kkonganti@1 56 withName: 'SOURMASH_SKETCH' {
kkonganti@1 57 ext.args = addParamsToSummary(
kkonganti@1 58 loadThisFunction("${params.toolshelp}${params.fs}sourmashsketch.nf").sourmashsketchHelp(params).helpparams
kkonganti@1 59 )
kkonganti@1 60 }
kkonganti@1 61 }
kkonganti@1 62
kkonganti@1 63 if (params.sourmashgather_run) {
kkonganti@1 64 withName: 'SOURMASH_GATHER' {
kkonganti@1 65 ext.args = addParamsToSummary(
kkonganti@1 66 loadThisFunction("${params.toolshelp}${params.fs}sourmashgather.nf").sourmashgatherHelp(params).helpparams
kkonganti@1 67 )
kkonganti@1 68
kkonganti@1 69 if (params.sfhpy_run) {
kkonganti@1 70 ext.args2 = addParamsToSummary(
kkonganti@1 71 loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
kkonganti@1 72 )
kkonganti@1 73 }
kkonganti@1 74 }
kkonganti@1 75 }
kkonganti@1 76
kkonganti@1 77 if (params.sourmashsearch_run) {
kkonganti@1 78 withName: 'SOURMASH_SEARCH' {
kkonganti@1 79 ext.args = addParamsToSummary(
kkonganti@1 80 loadThisFunction("${params.toolshelp}${params.fs}sourmashsearch.nf").sourmashsearchHelp(params).helpparams
kkonganti@1 81 )
kkonganti@1 82
kkonganti@1 83 if (params.sfhpy_run) {
kkonganti@1 84 ext.args2 = addParamsToSummary(
kkonganti@1 85 loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
kkonganti@1 86 )
kkonganti@1 87 }
kkonganti@1 88 }
kkonganti@1 89 }
kkonganti@1 90
kkonganti@1 91 if (params.kmaindex_run) {
kkonganti@1 92 withName: 'KMA_INDEX' {
kkonganti@1 93 ext.args = addParamsToSummary(
kkonganti@1 94 loadThisFunction("${params.toolshelp}${params.fs}kmaindex.nf").kmaindexHelp(params).helpparams
kkonganti@1 95 )
kkonganti@1 96 }
kkonganti@1 97 }
kkonganti@1 98
kkonganti@1 99 if (params.kmaalign_run) {
kkonganti@1 100 withName: 'KMA_ALIGN' {
kkonganti@1 101 ext.args = addParamsToSummary(
kkonganti@1 102 loadThisFunction("${params.toolshelp}${params.fs}kmaalign.nf").kmaalignHelp(params).helpparams
kkonganti@1 103 )
kkonganti@1 104 }
kkonganti@1 105 }
kkonganti@1 106
kkonganti@1 107 if (params.salmonidx_run){
kkonganti@1 108 withName: 'SALMON_INDEX' {
kkonganti@1 109 ext.args = addParamsToSummary(
kkonganti@1 110 loadThisFunction("${params.toolshelp}${params.fs}salmonidx.nf").salmonidxHelp(params).helpparams
kkonganti@1 111 )
kkonganti@1 112 }
kkonganti@1 113 }
kkonganti@1 114
kkonganti@1 115 withName: 'OTF_GENOME' {
kkonganti@1 116 errorStrategy = 'ignore'
kkonganti@1 117 }
kkonganti@1 118
kkonganti@1 119 }
kkonganti@1 120
kkonganti@1 121
kkonganti@1 122 // Parse the default params
kkonganti@1 123 def loadThisFunction (func_file) {
kkonganti@1 124 GroovyShell grvy_sh = new GroovyShell()
kkonganti@1 125 def func = grvy_sh.parse(new File ( func_file ) )
kkonganti@1 126 return func
kkonganti@1 127 }
kkonganti@1 128
kkonganti@1 129 // Method to add relevant final parameters to summary log
kkonganti@1 130 def addParamsToSummary(Map params_to_add = [:]) {
kkonganti@1 131
kkonganti@1 132 if (!params_to_add.isEmpty()) {
kkonganti@1 133 def not_null_params_to_add = params_to_add.findAll {
kkonganti@1 134 it.value.clivalue != null &&
kkonganti@1 135 it.value.clivalue != '[:]' &&
kkonganti@1 136 it.value.clivalue != ''
kkonganti@1 137 }
kkonganti@1 138
kkonganti@1 139 params.logtheseparams += not_null_params_to_add.keySet().toList()
kkonganti@1 140
kkonganti@1 141 return not_null_params_to_add.collect {
kkonganti@1 142 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
kkonganti@1 143 }.join(' ').trim()
kkonganti@1 144 }
kkonganti@1 145 return 1
kkonganti@1 146 }