Mercurial > repos > galaxytrakr > hfp_bettercallsal_awsbatch
comparison 1.0.0/nextflow.config @ 0:801b85b03a17 draft default tip
planemo upload
| author | galaxytrakr |
|---|---|
| date | Thu, 28 May 2026 20:31:42 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:801b85b03a17 |
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| 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 // Set max queue size; local or cloud | |
| 37 // executor.queueSize = 50 | |
| 38 | |
| 39 //Finally include all compute profiles | |
| 40 profiles { | |
| 41 includeConfig "${pd}${fs}conf${fs}computeinfra.config" | |
| 42 } |