Mercurial > repos > kkonganti > cfsan_bettercallsal

comparison 0.6.1/workflows/conf/process/bettercallsal_db.process.config @ 11:749faef1caa9

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"planemo upload"
author kkonganti
date Tue, 05 Sep 2023 11:51:40 -0400
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10:1b9de878b04a 11:749faef1caa9
1 process {
2 withName: 'DB_PER_COMPUTED_SEROTYPE' {
3 ext.args = addParamsToSummary(
4 loadThisFunction("${params.toolshelp}${params.fs}wcomp.nf").wcompHelp(params).helpparams
5 )
6 }
7
8 withName: 'DB_PER_SNP_CLUSTER' {
9 ext.args = addParamsToSummary(
10 loadThisFunction("${params.toolshelp}${params.fs}wsnp.nf").wsnpHelp(params).helpparams
11 )
12 }
13
14 if (params.mashsketch_run) {
15 withName: 'MASH_SKETCH' {
16 ext.args = addParamsToSummary(
17 loadThisFunction("${params.toolshelp}${params.fs}mashsketch.nf").mashsketchHelp(params).helpparams
18 )
19 }
20 }
21
22 withName: 'SCAFFOLD_GENOMES' {
23 maxRetries = 5
24 publishDir = [
25 path: "${params.output}${params.fs}scaffold_genomes",
26 mode: "move",
27 overwrite: true,
28 saveAs: { filename -> filename ==~ /versions\.yml|genome_paths\.txt/ ? null : filename }
29 ]
30 }
31 }
32
33
34 // Parse the default params
35 def loadThisFunction (func_file) {
36 GroovyShell grvy_sh = new GroovyShell()
37 def func = grvy_sh.parse(new File ( func_file ) )
38 return func
39 }
40
41 // Method to add relevant final parameters to summary log
42 def addParamsToSummary(Map params_to_add = [:]) {
43
44 if (!params_to_add.isEmpty()) {
45 def not_null_params_to_add = params_to_add.findAll {
46 it.value.clivalue != null &&
47 it.value.clivalue != '[:]' &&
48 it.value.clivalue != ''
49 }
50
51 params.logtheseparams += not_null_params_to_add.keySet().toList()
52
53 return not_null_params_to_add.collect {
54 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
55 }.join(' ').trim()
56 }
57 return 1
58 }