kkonganti@17: // Main driver script
kkonganti@17: manifest.mainScript = 'cpipes'
kkonganti@17: 
kkonganti@17: def fs = File.separator
kkonganti@17: def pd = "${projectDir}"
kkonganti@17: 
kkonganti@17: // Global parameters
kkonganti@17: includeConfig "${pd}${fs}conf${fs}manifest.config"
kkonganti@17: includeConfig "${pd}${fs}conf${fs}base.config"
kkonganti@17: 
kkonganti@17: // Include FASTQ config to prepare for a case when the entry point is 
kkonganti@17: // FASTQ metadata CSV or FASTQ input directory
kkonganti@17: includeConfig "${pd}${fs}conf${fs}fastq.config"
kkonganti@17: 
kkonganti@17: if (params.pipeline != null) {
kkonganti@17:     try {
kkonganti@17:         includeConfig "${params.workflowsconf}${fs}${params.pipeline}.config"
kkonganti@17:     } catch (Exception e) {
kkonganti@17:         System.err.println('-'.multiply(params.linewidth) + "\n" +
kkonganti@17:             "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
kkonganti@17:             '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
kkonganti@17:             "default pipeline configuration. Please provide a pipeline \n" +
kkonganti@17:             "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
kkonganti@17:         System.exit(1)
kkonganti@17:     }
kkonganti@17: }
kkonganti@17: 
kkonganti@17: // Include modules' config last.
kkonganti@17: includeConfig "${pd}${fs}conf${fs}logtheseparams.config"
kkonganti@17: includeConfig "${pd}${fs}conf${fs}modules.config"
kkonganti@17: 
kkonganti@17: // Nextflow runtime profiles
kkonganti@17: conda.cacheDir = "${pd}${fs}kondagac_cache"
kkonganti@17: singularity.cacheDir = "${pd}${fs}cingularitygac_cache"
kkonganti@17: 
kkonganti@17: // Set max queue size; local or cloud
kkonganti@17: // executor.queueSize  = 50
kkonganti@17: 
kkonganti@17: //Finally include all compute profiles
kkonganti@17: profiles {
kkonganti@17:     includeConfig "${pd}${fs}conf${fs}computeinfra.config"
kkonganti@17: }