Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.6.1/workflows/conf/process/bettercallsal_db.process.config @ 11:749faef1caa9
"planemo upload"
| author | kkonganti |
|---|---|
| date | Tue, 05 Sep 2023 11:51:40 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 process { |
| kkonganti@11 | 2 withName: 'DB_PER_COMPUTED_SEROTYPE' { |
| kkonganti@11 | 3 ext.args = addParamsToSummary( |
| kkonganti@11 | 4 loadThisFunction("${params.toolshelp}${params.fs}wcomp.nf").wcompHelp(params).helpparams |
| kkonganti@11 | 5 ) |
| kkonganti@11 | 6 } |
| kkonganti@11 | 7 |
| kkonganti@11 | 8 withName: 'DB_PER_SNP_CLUSTER' { |
| kkonganti@11 | 9 ext.args = addParamsToSummary( |
| kkonganti@11 | 10 loadThisFunction("${params.toolshelp}${params.fs}wsnp.nf").wsnpHelp(params).helpparams |
| kkonganti@11 | 11 ) |
| kkonganti@11 | 12 } |
| kkonganti@11 | 13 |
| kkonganti@11 | 14 if (params.mashsketch_run) { |
| kkonganti@11 | 15 withName: 'MASH_SKETCH' { |
| kkonganti@11 | 16 ext.args = addParamsToSummary( |
| kkonganti@11 | 17 loadThisFunction("${params.toolshelp}${params.fs}mashsketch.nf").mashsketchHelp(params).helpparams |
| kkonganti@11 | 18 ) |
| kkonganti@11 | 19 } |
| kkonganti@11 | 20 } |
| kkonganti@11 | 21 |
| kkonganti@11 | 22 withName: 'SCAFFOLD_GENOMES' { |
| kkonganti@11 | 23 maxRetries = 5 |
| kkonganti@11 | 24 publishDir = [ |
| kkonganti@11 | 25 path: "${params.output}${params.fs}scaffold_genomes", |
| kkonganti@11 | 26 mode: "move", |
| kkonganti@11 | 27 overwrite: true, |
| kkonganti@11 | 28 saveAs: { filename -> filename ==~ /versions\.yml|genome_paths\.txt/ ? null : filename } |
| kkonganti@11 | 29 ] |
| kkonganti@11 | 30 } |
| kkonganti@11 | 31 } |
| kkonganti@11 | 32 |
| kkonganti@11 | 33 |
| kkonganti@11 | 34 // Parse the default params |
| kkonganti@11 | 35 def loadThisFunction (func_file) { |
| kkonganti@11 | 36 GroovyShell grvy_sh = new GroovyShell() |
| kkonganti@11 | 37 def func = grvy_sh.parse(new File ( func_file ) ) |
| kkonganti@11 | 38 return func |
| kkonganti@11 | 39 } |
| kkonganti@11 | 40 |
| kkonganti@11 | 41 // Method to add relevant final parameters to summary log |
| kkonganti@11 | 42 def addParamsToSummary(Map params_to_add = [:]) { |
| kkonganti@11 | 43 |
| kkonganti@11 | 44 if (!params_to_add.isEmpty()) { |
| kkonganti@11 | 45 def not_null_params_to_add = params_to_add.findAll { |
| kkonganti@11 | 46 it.value.clivalue != null && |
| kkonganti@11 | 47 it.value.clivalue != '[:]' && |
| kkonganti@11 | 48 it.value.clivalue != '' |
| kkonganti@11 | 49 } |
| kkonganti@11 | 50 |
| kkonganti@11 | 51 params.logtheseparams += not_null_params_to_add.keySet().toList() |
| kkonganti@11 | 52 |
| kkonganti@11 | 53 return not_null_params_to_add.collect { |
| kkonganti@11 | 54 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}" |
| kkonganti@11 | 55 }.join(' ').trim() |
| kkonganti@11 | 56 } |
| kkonganti@11 | 57 return 1 |
| kkonganti@11 | 58 } |