Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.1.0/nextflow.config @ 0:c8597e9e1a97
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 27 Nov 2023 12:37:44 -0500 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@0 | 1 def fs = File.separator |
| kkonganti@0 | 2 def pd = "${projectDir}" |
| kkonganti@0 | 3 |
| kkonganti@0 | 4 // Global parameters |
| kkonganti@0 | 5 includeConfig "${pd}${fs}conf${fs}manifest.config" |
| kkonganti@0 | 6 includeConfig "${pd}${fs}conf${fs}base.config" |
| kkonganti@0 | 7 |
| kkonganti@0 | 8 // Include FASTQ config to prepare for a case when the entry point is |
| kkonganti@0 | 9 // FASTQ metadata CSV or FASTQ input directory |
| kkonganti@0 | 10 includeConfig "${pd}${fs}conf${fs}fastq.config" |
| kkonganti@0 | 11 |
| kkonganti@0 | 12 if (params.pipeline != null) { |
| kkonganti@0 | 13 try { |
| kkonganti@0 | 14 includeConfig "${params.workflowsconf}${fs}${params.pipeline}.config" |
| kkonganti@0 | 15 } catch (Exception e) { |
| kkonganti@0 | 16 System.err.println('-'.multiply(params.linewidth) + "\n" + |
| kkonganti@0 | 17 "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" + |
| kkonganti@0 | 18 '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " + |
| kkonganti@0 | 19 "default pipeline configuration. Please provide a pipeline \n" + |
| kkonganti@0 | 20 "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n" + e) |
| kkonganti@0 | 21 System.exit(1) |
| kkonganti@0 | 22 } |
| kkonganti@0 | 23 } |
| kkonganti@0 | 24 |
| kkonganti@0 | 25 // Include modules' config last. |
| kkonganti@0 | 26 includeConfig "${pd}${fs}conf${fs}logtheseparams.config" |
| kkonganti@0 | 27 includeConfig "${pd}${fs}conf${fs}modules.config" |
| kkonganti@0 | 28 |
| kkonganti@0 | 29 // Nextflow runtime profiles |
| kkonganti@0 | 30 conda.cacheDir = "${pd}${fs}kondagac_cache" |
| kkonganti@0 | 31 singularity.cacheDir = "${pd}${fs}cingularitygac_cache" |
| kkonganti@0 | 32 |
| kkonganti@0 | 33 profiles { |
| kkonganti@0 | 34 includeConfig "${pd}${fs}conf${fs}computeinfra.config" |
| kkonganti@0 | 35 } |