Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.7.0/nextflow.config @ 17:0e7a0053e4a6
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 10:42:02 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@17 | 1 // Main driver script |
| kkonganti@17 | 2 manifest.mainScript = 'cpipes' |
| kkonganti@17 | 3 |
| kkonganti@17 | 4 def fs = File.separator |
| kkonganti@17 | 5 def pd = "${projectDir}" |
| kkonganti@17 | 6 |
| kkonganti@17 | 7 // Global parameters |
| kkonganti@17 | 8 includeConfig "${pd}${fs}conf${fs}manifest.config" |
| kkonganti@17 | 9 includeConfig "${pd}${fs}conf${fs}base.config" |
| kkonganti@17 | 10 |
| kkonganti@17 | 11 // Include FASTQ config to prepare for a case when the entry point is |
| kkonganti@17 | 12 // FASTQ metadata CSV or FASTQ input directory |
| kkonganti@17 | 13 includeConfig "${pd}${fs}conf${fs}fastq.config" |
| kkonganti@17 | 14 |
| kkonganti@17 | 15 if (params.pipeline != null) { |
| kkonganti@17 | 16 try { |
| kkonganti@17 | 17 includeConfig "${params.workflowsconf}${fs}${params.pipeline}.config" |
| kkonganti@17 | 18 } catch (Exception e) { |
| kkonganti@17 | 19 System.err.println('-'.multiply(params.linewidth) + "\n" + |
| kkonganti@17 | 20 "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" + |
| kkonganti@17 | 21 '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " + |
| kkonganti@17 | 22 "default pipeline configuration. Please provide a pipeline \n" + |
| kkonganti@17 | 23 "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n") |
| kkonganti@17 | 24 System.exit(1) |
| kkonganti@17 | 25 } |
| kkonganti@17 | 26 } |
| kkonganti@17 | 27 |
| kkonganti@17 | 28 // Include modules' config last. |
| kkonganti@17 | 29 includeConfig "${pd}${fs}conf${fs}logtheseparams.config" |
| kkonganti@17 | 30 includeConfig "${pd}${fs}conf${fs}modules.config" |
| kkonganti@17 | 31 |
| kkonganti@17 | 32 // Nextflow runtime profiles |
| kkonganti@17 | 33 conda.cacheDir = "${pd}${fs}kondagac_cache" |
| kkonganti@17 | 34 singularity.cacheDir = "${pd}${fs}cingularitygac_cache" |
| kkonganti@17 | 35 |
| kkonganti@17 | 36 // Set max queue size; local or cloud |
| kkonganti@17 | 37 // executor.queueSize = 50 |
| kkonganti@17 | 38 |
| kkonganti@17 | 39 //Finally include all compute profiles |
| kkonganti@17 | 40 profiles { |
| kkonganti@17 | 41 includeConfig "${pd}${fs}conf${fs}computeinfra.config" |
| kkonganti@17 | 42 } |