hfp_centriflaken_awsbatch: 0.4.2/workflows/conf/process/spades

planemo upload

comparison

equal deleted inserted replaced

--1:000000000000
+:082e0091e813
+process {
+withName: 'SPADES_ASSEMBLE' {
+ext.args = addParamsToSummary(
+loadThisFunction("${params.toolshelp}${params.fs}spades.nf").spadesHelp(params).helpparams
+)
+}
+}
+// Method to instantiate a new function parser
+// Need to refactor using ScriptParser... another day
+def loadThisFunction (func_file) {
+GroovyShell grvy_sh = new GroovyShell()
+def func = grvy_sh.parse(new File ( func_file ) )
+return func
+}
+// Method to add relevant final parameters to summary log
+def addParamsToSummary(Map params_to_add = [:]) {
+if (!params_to_add.isEmpty()) {
+def not_null_params_to_add = params_to_add.findAll {
+it.value.clivalue != null &&
+it.value.clivalue != '[:]' &&
+it.value.clivalue != ''
+}
+params.logtheseparams += not_null_params_to_add.keySet().toList()
+return not_null_params_to_add.collect {
+"${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
+}.join(' ').trim()
+}
+return 1
+}

Mercurial > repos > galaxytrakr > hfp_centriflaken_awsbatch