Mercurial > repos > kkonganti > cfsan_centriflaken

annotate 0.4.2/workflows/conf/process/centriflaken.process.config @ 105:52045ea4679d

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"planemo upload"
author kkonganti
date Thu, 27 Jun 2024 14:17:26 -0400
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kkonganti@105 1 process {
kkonganti@105 2 withName: 'SEQKIT_SEQ' {
kkonganti@105 3 ext.args = [
kkonganti@105 4 params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
kkonganti@105 5 ].join(' ').trim()
kkonganti@105 6 }
kkonganti@105 7
kkonganti@105 8 if (params.seqkit_grep_on) {
kkonganti@105 9 withName: 'SEQKIT_GREP' {
kkonganti@105 10 ext.args = addParamsToSummary(
kkonganti@105 11 loadThisFunction("${params.toolshelp}${params.fs}seqkitgrep.nf").seqkitgrepHelp(params).helpparams
kkonganti@105 12 )
kkonganti@105 13 }
kkonganti@105 14 }
kkonganti@105 15
kkonganti@105 16 withName: 'CENTRIFUGE_CLASSIFY' {
kkonganti@105 17 ext.args = addParamsToSummary(
kkonganti@105 18 loadThisFunction("${params.toolshelp}${params.fs}centrifuge.nf").centrifugeHelp(params).helpparams
kkonganti@105 19 )
kkonganti@105 20 }
kkonganti@105 21
kkonganti@105 22 withName: 'KRAKEN2_CLASSIFY' {
kkonganti@105 23 ext.args = addParamsToSummary(
kkonganti@105 24 loadThisFunction("${params.toolshelp}${params.fs}kraken2.nf").kraken2Help(params).helpparams
kkonganti@105 25 )
kkonganti@105 26 }
kkonganti@105 27
kkonganti@105 28 withName: 'FLYE_ASSEMBLE' {
kkonganti@105 29 errorStrategy = 'ignore'
kkonganti@105 30 ext.args = addParamsToSummary(
kkonganti@105 31 loadThisFunction("${params.toolshelp}${params.fs}flye.nf").flyeHelp(params).helpparams
kkonganti@105 32 )
kkonganti@105 33 }
kkonganti@105 34
kkonganti@105 35 if (params.ectyper_run) {
kkonganti@105 36 withName: 'ECTYPER' {
kkonganti@105 37 ext.when = params.ectyper_run
kkonganti@105 38 ext.args = addParamsToSummary(
kkonganti@105 39 loadThisFunction("${params.toolshelp}${params.fs}ectyper.nf").ectyperHelp(params).helpparams
kkonganti@105 40 )
kkonganti@105 41 }
kkonganti@105 42 }
kkonganti@105 43
kkonganti@105 44 withName: 'SEROTYPEFINDER' {
kkonganti@105 45 ext.when = params.serotypefinder_run
kkonganti@105 46 ext.args = addParamsToSummary(
kkonganti@105 47 loadThisFunction("${params.toolshelp}${params.fs}serotypefinder.nf").serotypefinderHelp(params).helpparams
kkonganti@105 48 )
kkonganti@105 49 }
kkonganti@105 50
kkonganti@105 51 withName: 'SEQSERO2' {
kkonganti@105 52 ext.when = params.seqsero2_run
kkonganti@105 53 ext.args = addParamsToSummary(
kkonganti@105 54 loadThisFunction("${params.toolshelp}${params.fs}seqsero2.nf").seqsero2Help(params).helpparams
kkonganti@105 55 )
kkonganti@105 56 }
kkonganti@105 57
kkonganti@105 58 withName: 'MLST' {
kkonganti@105 59 ext.when = params.mlst_run
kkonganti@105 60 ext.args = addParamsToSummary(
kkonganti@105 61 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
kkonganti@105 62 )
kkonganti@105 63 }
kkonganti@105 64
kkonganti@105 65 if (params.amrfinderplus_run) {
kkonganti@105 66 withName: 'AMRFINDERPLUS_RUN' {
kkonganti@105 67 ext.when = params.amrfinderplus_run
kkonganti@105 68 ext.args = addParamsToSummary(
kkonganti@105 69 loadThisFunction("${params.toolshelp}${params.fs}amrfinderplus.nf").amrfinderplusHelp(params).helpparams
kkonganti@105 70 )
kkonganti@105 71 }
kkonganti@105 72 }
kkonganti@105 73
kkonganti@105 74 withName: 'ABRICATE_RUN' {
kkonganti@105 75 ext.when = params.abricate_run
kkonganti@105 76 ext.args = addParamsToSummary(
kkonganti@105 77 loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
kkonganti@105 78 )
kkonganti@105 79 }
kkonganti@105 80
kkonganti@105 81 withName: 'ABRICATE_SUMMARY' {
kkonganti@105 82 ext.when = params.abricate_summary_run
kkonganti@105 83 }
kkonganti@105 84 }
kkonganti@105 85
kkonganti@105 86 // Method to instantiate a new function parser
kkonganti@105 87 // Need to refactor using ScriptParser... another day
kkonganti@105 88 def loadThisFunction (func_file) {
kkonganti@105 89 GroovyShell grvy_sh = new GroovyShell()
kkonganti@105 90 def func = grvy_sh.parse(new File ( func_file ) )
kkonganti@105 91 return func
kkonganti@105 92 }
kkonganti@105 93
kkonganti@105 94 // Method to add relevant final parameters to summary log
kkonganti@105 95 def addParamsToSummary(Map params_to_add = [:]) {
kkonganti@105 96
kkonganti@105 97 if (!params_to_add.isEmpty()) {
kkonganti@105 98 def not_null_params_to_add = params_to_add.findAll {
kkonganti@105 99 it.value.clivalue != null &&
kkonganti@105 100 it.value.clivalue != '[:]' &&
kkonganti@105 101 it.value.clivalue != ''
kkonganti@105 102 }
kkonganti@105 103
kkonganti@105 104 params.logtheseparams += not_null_params_to_add.keySet().toList()
kkonganti@105 105
kkonganti@105 106 return not_null_params_to_add.collect {
kkonganti@105 107 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
kkonganti@105 108 }.join(' ').trim()
kkonganti@105 109 }
kkonganti@105 110 return 1
kkonganti@105 111 }