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comparison 0.5.0/nextflow.config @ 0:97cd2f532efe

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planemo upload
author kkonganti
date Mon, 31 Mar 2025 14:50:40 -0400
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-1:000000000000 0:97cd2f532efe
1 // Main driver script
2 manifest.mainScript = 'cpipes'
3
4 def fs = File.separator
5 def pd = "${projectDir}"
6
7 // Global parameters
8 includeConfig "${pd}${fs}conf${fs}manifest.config"
9 includeConfig "${pd}${fs}conf${fs}base.config"
10
11 // Include FASTQ config to prepare for a case when the entry point is
12 // FASTQ metadata CSV or FASTQ input directory
13 includeConfig "${pd}${fs}conf${fs}fastq.config"
14
15 if (params.pipeline != null) {
16 try {
17 includeConfig "${params.workflowsconf}${fs}${params.pipeline}.config"
18 } catch (Exception e) {
19 System.err.println('-'.multiply(params.linewidth) + "\n" +
20 "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
21 '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
22 "default pipeline configuration. Please provide a pipeline \n" +
23 "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
24 System.exit(1)
25 }
26 }
27
28 // Include modules' config last.
29 includeConfig "${pd}${fs}conf${fs}logtheseparams.config"
30 includeConfig "${pd}${fs}conf${fs}modules.config"
31
32 // Nextflow runtime profiles
33 conda.cacheDir = "${pd}${fs}kondagac_cache"
34 singularity.cacheDir = "${pd}${fs}cingularitygac_cache"
35
36 // Clean up after successfull run
37 // cleanup = true
38
39 profiles {
40 includeConfig "${pd}${fs}conf${fs}computeinfra.config"
41 }