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