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