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0
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1 process {
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2 withName: 'DB_PER_COMPUTED_SEROTYPE' {
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3 ext.args = addParamsToSummary(
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4 loadThisFunction("${params.toolshelp}${params.fs}wcomp.nf").wcompHelp(params).helpparams
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5 )
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6 }
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7
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8 withName: 'DB_PER_SNP_CLUSTER' {
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9 ext.args = addParamsToSummary(
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10 loadThisFunction("${params.toolshelp}${params.fs}wsnp.nf").wsnpHelp(params).helpparams
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11 )
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12 }
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13
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14 if (params.mashsketch_run) {
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15 withName: 'MASH_SKETCH' {
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16 ext.args = addParamsToSummary(
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17 loadThisFunction("${params.toolshelp}${params.fs}mashsketch.nf").mashsketchHelp(params).helpparams
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18 )
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19 }
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20 }
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21
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22 withName: 'SCAFFOLD_GENOMES' {
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23 maxRetries = 5
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24 publishDir = [
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25 path: "${params.output}${params.fs}scaffold_genomes",
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26 mode: "move",
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27 overwrite: true,
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28 saveAs: { filename -> filename ==~ /versions\.yml|genome_paths\.txt/ ? null : filename }
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29 ]
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30 }
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31 }
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32
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33
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34 // Parse the default params
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35 def loadThisFunction (func_file) {
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36 GroovyShell grvy_sh = new GroovyShell()
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37 def func = grvy_sh.parse(new File ( func_file ) )
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38 return func
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39 }
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40
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41 // Method to add relevant final parameters to summary log
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42 def addParamsToSummary(Map params_to_add = [:]) {
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43
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44 if (!params_to_add.isEmpty()) {
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45 def not_null_params_to_add = params_to_add.findAll {
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46 it.value.clivalue != null &&
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47 it.value.clivalue != '[:]' &&
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48 it.value.clivalue != ''
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49 }
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50
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51 params.logtheseparams += not_null_params_to_add.keySet().toList()
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52
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53 return not_null_params_to_add.collect {
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54 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
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55 }.join(' ').trim()
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56 }
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57 return 1
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58 }
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